


How far down the rabbit hole are you willing to go?

by BlindedKnight



Category: Doctor Who (2005), The Matrix (Movies)
Genre: Alternate Universe - The Matrix, F/M, Science Fiction
Language: English
Status: Completed
Published: 2016-05-18
Updated: 2016-07-22
Packaged: 2018-06-09 04:04:40
Rating: Explicit
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 32
Words: 37,665
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/6889234
Author URL: https://archiveofourown.org/users/BlindedKnight/pseuds/BlindedKnight
Summary: <blockquote class="userstuff">
              <p>“Ugh, why do you drones like to keep calling me that? I'm the Doctor and you know exactly where they are, gone from your little metal hands being picked up right now.” He smirked looking around at the group of heavily armed men before staring towards the camera a slight grin forming.</p><p>“We will find them Mr Smith. You're breaking the peace --”</p><p>He frowned shaking his head to the agent, “To hell with that agreement, you know even my side dislikes me for what I do. They all need to be set free, including you. I bet to you it even gets boring in here, especially with dealing with people like me.” He sighed, “Anyway enough talk you've almost got my signal haven't you?”</p><p>“Yes.”</p><p>“Time for running then.”</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> I had this idea of the Doctor deal with a matrix like world which then turned into an alternate universe story. This is the first chapter as I'm getting feels to how people might enjoy it. 
> 
> So who's up for going down the rabbit hole with me?

_A hostile stand off late last night resulted in 5 dead and dozens injured as authorities attempted to subdue the criminal known as The Doctor, who managed to once again to flee this time managing to kidnap a young married couple._ The radio blared out as Danny and Clara sat in the car in the middle of rush hour traffic as he drove her home.

“Wow two people this time, that man is starting to get cocky.” Danny shook his head turning the volume down, “There's going to be one day he slips and they'll get him, lock him up in a box.”

Clara sighed a little, Dannys arrogance sometimes got the better of him, “Not without a fair trial.”

Danny laughed looking at her, “A fair trial? Clara he's murdered people, hell the only person he's kidnapped to ever come back doesn't remember a damn thing. Who knows what he has done to that poor woman.”

“But she was fine and last time I heard she got married, so it must not have been that bad.”

“Then why does she not remember anything if it wasn't that bad?”

Clara shrugged, “Maybe she's protecting him?”

“Protecting a murderer? Clara honestly.”

Clara almost opened her mouth to make a comment but thought against it, she didn't want a full out war in the small vehicle on such a silly topic. Though it was no small feat for one man dealing with a mass of policemen while managing to sneak away with one let along two people in tow, something didn't seem right. She was lost in thought till Danny brought her back to reality as they arrived to her flat.

“Want me to come up with you?” he smiled to her.

Clara giggled and shook her head, knowing the intent of the question, “Sorry tons of marking to do tonight.”

“Well then stop giving them so much homework.”

“You need to stop giving yours too little,” she grinned leaning over giving him a small kiss on the lips before exiting the car, “see you tomorrow.”

 

Clara sat down, after promptly changing into her pajamas and brewing a fresh cuppa, with the large pile of writing assignments in front of her turning on the television for a bit of background noise as she started reading over the pile. She was half way through when she looked up noticing the news was on and reporting about the Doctor showing pictures of the condemned building the incident happened in and also the couple that he kidnapped this time, Amy and Rory Williams.

The news broadcaster straightened himself up looking straight to the camera, _We also have, thanks to an anonymous donator, a video of the ordeal. This is just a notice it might be very distressful to the viewing audience._ Claras interest perked as this was the first time that any pictures, let alone a video, was ever shown of the Doctor to her knowledge.

The very grainy black and white video started up, very noticeably that it is coming from one of the officers, showing a good number of heavily armored and armed police officers with a suited man standing around a very young lanky man with a big poof of dark hair almost covering his eyes casually holding his arms up.

“ _Mr. Smith, where are they?”_ , the agents voice droned.

“ _Ugh, why do you drones like to keep calling me that? I'm the Doctor and you know exactly where they are, gone from your little metal hands being picked up right now.”_ He smirked looking around at the group of heavily armed men before staring towards the camera a slight grin forming.

“ _We will find them Mr Smith. You're breaking the peace --”_

He frowned shaking his head to the agent, “ _To hell with that agreement, you know even my side dislikes me for what I do. They all need to be set free, including you. I bet to you it even gets boring in here, especially with dealing with people like me.”_ He sighed, _“Anyway enough talk you've almost got my signal haven't you?”_

“ _Yes.”_

“ _Time for running then.”_ He slicked back the quiff of hair, tugged on the lapels of his jacket before rushing straight at the camera which blacked out as soon as the gunfire happened for a few seconds ending the video returning back to the broadcaster whose eyes were wide with surprise before returning to the broadcast.

 

Clara had almost slid off the sofa as she had been watching it so intently, the question rolled around her head: They all need to be set free? What did that mean? The whole conversation made no sense, his signal? He was standing right there. She shook her head, it was all crazy and something she shouldn't lose sleep or ignore marking papers over, till she of course reached Courtney Woods' paper, the girl had quite the imagination especially when given free reign on the writing subject which as Clara read was on an interesting topic; What is the matrix?

Clara raised an eyebrow as she read on, some of what she was reading was so far fetched, typical of her character, but some of it made sense as there was a video out there of the Doctor and this man in black. She was definitely going to have another talk with Courtney over this topic especially when the assignment was to write a topic of non-fiction not science fiction but it intrigued her as it was starting to place a lot of questions into her head. Why was the Doctor doing what he was doing and what was the matrix?

 


	2. Chapter 2

Clara took Courtney off the side as the bell rang, the first time she has ever done such a thing which surprised the both of them. “I need to talk to you about your paper after lunch will you come by please?”

Courtney smirked, shaking her head a little, “Saying you'll get your boyfriend after me I know I won't have a choice.”

Clara frowned, even though it was pretty much near public knowledge that her and Danny were dating she still had to pretend they weren't, “Please don't call Mr. Pink that, we all know better.”

She snorted, “Sure whatever Miss Oswald I need to get to next class.”

 

Clara waited patiently in her room, she of course had Danny keep a look out in the yard to see if Courtney was avoiding her as usual but to her surprise there was a knock on the door frame to which Courtney stood smirking.

“Let me text Dan-er Mr. Pink so he knows to stop looking for you.”

Courtney grinned slyly, “Or don't and keep him running around. It's why I decided to show up this time.”

Clara smirked, deleting the message she was about to send to Danny, “Alright, so you know why I asked you to be here?”

“Poor writing and not the right subject for the assignment?” She finally walked in standing next to Claras desk.

She was slightly taken aback, this was the first time Courtney didn't beat around the bush, “Yes but I'm going to give you a decent grade for it if you help me.”

Courtney smirked giving away that she knew, “You saw the video didn't you?”

“Yes and if I didn't I would have contacted your parents questioning what you've been up to because before that video I thought that man was dangerous now it just brought up a lot of questions.”

“You want to know more?”

Clara nodded and handed over her already graded paper, “You seem to know it all, saying you're the one that figured out Mr Pink and I were dating.”

Courtney laughed, “It wasn't that hard to see Miss Oswald. Speaking of which,” she reached over and pulled a post-it note from the pile writing down a URL handing it to her, “it's a lot of tin-foil hat stuff but kind of cool given how much stuff was proven right with the video.”

Clara looked slightly confused, “Tin-foil hat stuff?”

“Conspiracy theories, which will blow your mind.”

“Alright,” she looked to her watch noticing lunch period was almost done, “lunch is almost over but next time when I want non-fiction I expect it.”

Courtney smiled, “No guarantees Miss Oswald.”

Just as Courtney was exiting out of Claras room Danny came around surprised to see her already there, “Oh Courtney you were here, for the first time ever.”

“And now I'm leaving bye.”

Danny huffed and shook his head walking inside, “And to think that girl somehow changed.”

“Just for lunch period.” Clara smirked.

“So any plans tonight?”

“Just dinner with my boyfriend at eight.” Clara smiled and then started to giggle.

Danny smiled leaning over sneaking in a quick kiss to her cheek before the bell rang, “See you then.”

 

\------

 

 

Clara managed to beat the rush, thanks to riding a motorcycle in between the cars stuck in traffic, and rushed inside grabbing her laptop opening up the website that Courtney had wrote down. The site loaded fairly quickly, with good reason it looked like it came from the late 90's dark blue background with black font luckily it was decent looking regardless of the age. She scrolled down till the words “Who is the Doctor?” in a headlining text appeared. After clicking the link, she scrolled through the giant mass of pictures till she reached the end of the stills from the video the other night.

The hour she was going to peruse the website turned into nearly four before she realized what time it was and she was going to be very, very late for her dinner date with Danny. Rushing out she forgot to close the lid to the laptop leaving it on and still opened on the page she had spent those hours on.

 

\----

 

A figure sat in the darkness looking at the multiple monitors streaming the green code, leaning forward he typed at the keyboard the ringing phone line started up in his headset which picked up after a few short rings.

The young English voice answered, _'New one already?'_

The man at the console replied in a very apparent American accent, “Oh yeah she was reading your page for almost four hours.”

_'Oh my that's a new record. Where she is headed?'_

“To be fashionably late to a dinner date.”

The man on the other end chuckled, _'Amusing. You keep a sharp eye out Jack, Idris says that agents have been going wild after I deployed the video.'_

“Why did you decide to release that anyway? You know everyone's gonna know your face now.”

_'Just needed a little more excitement in my life.'_

“More like a death wish.”

_'We'll talk about this later I have a rabbit to spy on.'_

“Well you do your thing Alice, I'll be here.”

 

\----

 

Clara rushed in smiling at Danny as he sat at the table, “So, so sorry I got caught up in something.”

Danny smirked, “Hopefully not groaning over another assignment Courtney did?”

“No, no.” She paused thinking if she should admit she was staring at a conspiracy site of the Doctor and decided against it reminding herself of the discussion in the car the other day. “Couldn't decide on what to wear.” She casually smiled glancing over to one of the tables near the far wall as she felt eyes on her but saw no one directly staring at her.

Danny turned looking around in the same direction she did and turned back looking at her confused, “Everything alright?”

“Yeah, yeah thought someone was watching me.”

Danny smirked, “Only me.”

 

 

The Doctor sighed slouching more in his chair watching the couple as the waiter came by to get their order. _Damn it don't like the looks of the boyfriend_ , he thought.

The twinge of a feminine voice poked at his mind almost like a subconscious, _'Why not?'_

He narrowed his eyes focusing on Danny watching how he held himself and all his other mannerisms, _'Possible soldier? Indoctrinated; won't let her go and will very easily snitch the moment he knows.'_

_'Still a challenge.'_

_'Yes it is but for later I still have to tend to Amy and Rory.'_

_'Of course my thief.'_

He smirked before standing up and started to slyly make his way near the table managing to catch her looking up , giving her a sly grin in return.

Danny looked over at her noticing the surprise on her face, “Clara whats wrong?”

Realizing her mouth was open she stuttered trying to figure out what to say, “Oh! Oh I-I thought I saw someone famous.” She turned looking down at the table her eyes still wide realizing he was here, in the same suit as in the video, which was a god awful brown that could make anyone including him stand out though seeing clearly how young he was it was clear Danny might have been right he was cocky, now she questioned whether she was right and that someone had been watching her and that it was him.

Danny looked around before looking back at Clara, “Don't see anyone.”

“Must have been my imagination.”

The Doctor smirked as he barely caught the conversation as he was nearing the exit, “Clever girl.”

 


	3. Chapter 3

Clara couldn't go to sleep, he was there, she didn't know if she should be frightened, excited or any other type of feeling appropriate to the situation that had happened. She didn't even tell Danny, didn't tell him that there was a criminal in the restaurant and just let him walk past. Which led up to more questions: Why did no one else see him? Why was he there anyway? What was up with that hideous jacket?

She let out a quick laugh as she asked herself that last question which made her finally give up on trying to sleep asleep for a bit longer going to the living room looking over the website once more. Intently reading at the section of the Doctor was just a name that many of person has taken till she scrolled down to the big thought that it was one person, using the fact that the agent that was in the video has been around for a long time but has never aged, which some very convincing pictures to follow up, was a far outstretch to the imagination.

She scrolled down some more noticing there was a chat room clicking the link the words, DO NOT USE YOUR REAL NAME THEY ARE WATCHING, was underlined, bold and in almost the biggest font one could use without having to scroll to see the whole sentence was used. Clara frowned a little concerned and questioning who was watching but decided to take the plunge, what was the worst that could happen, right?

 

Oswin (mibbit@2EF1383F.redacted) has joined the channel.

Three0Six: who seen that new Battlefield 1 trailer?

TacticalPlatypus: Fucking time growing tired of that futuristic cod shit

5ush1Lazor: ZEPPLINS ZOMG

 

Clara looked at the chat oddly, seemed more like a bunch of kids worrying over video games than conspiracy theorists in the chat.

 

Oswin: Hello?

DrD1sc0: Hello

BlindedKnight: Hi

Three0Six: So what do you think about Battlefield 1 Oswin?

Oswin: Sorry I don't play video games. A little old for that.

Three0Six: LOL

5ush1Lazor: LOL

Oswin: What's so funny?

BlindedKnight: LOL

DrD1sc0: Ignore them. They think it's amusing when someone says that.

Oswin: Why's that?

DrD1sc0: Ah only read the part about the Doctor?

Oswin: Yes.

TacticalPlatypus: Ugh here we go. Lrn2reed

 

Clara frowned, it was like her unruly classroom but she could deal with it, it was just a webpage and she can always turn it off and never return.

 

DrD1sc0: To save someone from having to see it for the millionth time, there's a tab at the bottom of this chat window with my name on it click it.

TacticalPlatypus: The old man finally learned PMs? Is the world ending?

DrD1sc0: stfu

TacticalPlatypus: :-O Language. MUM!

LadyMatrix: oh god knock it off. Be nice to the blues

TacticalPlatypus: Says the blue

TacticalPlatypus has been kicked from the channel by LadyMatrix. (Reason: You know what I mean.)

TacticalPlatypus (TacPlat@3EA1133F.redacted) has joined the channel.

TacticalPlatypus: OKOKOK

 

Clara laughed and noticed there was now a blinking tab with DrD1sc0's name on it, clicking on it brought up a whole new set of text.

 

DrD1sc0: Because this world isn't real – it's called the matrix. You're really in a pod connected to tubes being used like an energizer battery for robots while roaming a virtual world. That's why they find it amusing you're pretty much already playing a video game.

 

Clara was taken back by how blunt part of the answer was, she didn't know if he was joking or serious.

 

Oswin: That seems a little far fetched isn't it?

DrD1sc0: I'm just summing up what the website says. Sorry.

Oswin: Is it alright if I asked you questions? Seems like they want to talk about other things.

DrD1sc0: They're just kids. Smart kids, but kids none the less.

Oswin: I know the feeling.

DrD1sc0: You have kids?

Oswin: No, no. Teacher, probably just as bad.

DrD1sc0: I wouldn't know. Anyway questions. Fire away.

Oswin: I didn't see anything about that one woman Donna Noble what happened with her?

DrD1sco: Just rumors/theory; Something happened and she had to be put back into the matrix.

Oswin: Is the Doctor ever known to follow people?

DrD1sc0: Probably.

Oswin: Should I be worried?

DrD1sc0: About what?

Oswin: The Doctor? If he's following me.

DrD1sc0: You should be worried about agents, those men in black suits and your dreams.

Oswin: Why dreams?

DrD1sc0: Dreams are meant to be forgotten it's the easiest way for them to bug you and not question it.

Oswin: Did he kill all those people?

DrD1sc0: Which ones?

Oswin: The cops.

DrD1sc0: Maybe who knows.

Oswin: Anyway it's late, thanks a lot.

DrD1sc0: No problem good night.

 

The Doctor sat back in the jump seat, his old grey eyes looking at the code streaming Claras room watching her slide back under the covers going back to sleep. He looked over to a monitor that had golden code streaming down, “So what do you think?” He nodded seeing the reply, “We'll wait. Could very much be a trap saying she's this interested this quickly.” He stretched, yawning and ruffling his grey silver curls with his hands, “Sadly this old body thinks bed is a good idea as well.”

Jack strolled in, seeing him in the chair, “Still up?”

He looked over to Jack and nodded, “Yeah, she got into the chat. Was answering some of her questions.”

“Trap?”

“It's what I was thinking.” He slid out of the chair with a slight groan and another yawn, “I'm going to bed been a long day.”

Jack smirked sitting down in the still warm jump seat, “Three days.”

The Doctor paused and looked at him, “Really?”

He smiled placing the headset on his head, “You do it every time.”

“How soon are we going back by the way? I know you said we're running out of supplies.”

“Tomorrow.”

The Doctor nodded and made his way to his room closing the door locking it shut before falling face first into the bed groaning once more. Age was surely catching up with him and proving that he can't be as adventurous as he used to. Rolling over finding a comfortable place in the small lumps of his very used mattress his mind wondered about Clara, he was going to time about her to see if it's worth all the trouble.

 

**Notes for the Chapter:**

> sorry my 133t5p34k isn't up to snuff. But IRC is and mostly has been the playground of the hacking community - it would be something Neo would have poked around as well when he was doing his coding / info finding.


	4. Chapter 4

Jack walked off the ramp of the hovercraft before noticing a small group of guards and the head security officer glaring towards him. For supposedly being different from Zion, New Zion wasn't as accommodating as well whenever they landed. He sighed, he couldn't play dumb nor try to flirt the socks off any of them, walking over preparing himself for the bad news.

“We're following protocol so what is it this time? I landed too hard on the dock?”

The bald headed man glared at Jack, “He broke the peace agreement Jack.”

He raised his arms up in the air in defeat, that was something that everyone has know for ages, letting them fall to his side, “And what's different from before?”

“He's making huge waves, it was agreed that we would extract those that went to far reaches to find us out to know the truth.”

“Amy and Rory wanted out so I don't --”

He narrowed his eyes, “The video, Jack.”

Jack paused looking to the man, “It doesn't directly say anything.”

“Yes well the machines aren't exactly thrilled and you can never change their minds about it once it's set.”

Jack sighed, shaking his head, “Death sentence?”

“No we're taking the extracts.”

He raised his voice pointing towards his ship, “No you're not putting them back.”

“We're not. They're staying here.”

Jack pointed to himself, in desperation in trying to keep Amy and Rory with him, “I need a medic for my ship, especially with the Doctor.”

“Then he should have thought of the consequences.”

Jack groaned, rubbing his face trying to think, “Can I at least get a medic? A willing medic?”

“No.”

Crossing his arms he frowned, “So it is a death sentence because I can't properly treat him if he decides to self-extract.”

“I'm sorry Jack it was the only way. It was either this or letting the squids get your ship and kill you too and we need all the hovercraft in case we have another war.”

Jack shook his head, “This is such horseshit, you know it.”

“Now that's out of the way, can we board so we can take them?”

Jack sighed relenting to the situation that unfolded, “Saying there's five guards with arc guns pointed in my general direction I have no choice. Be silent about it I'm sure the Doctor is still sleeping.”

 

 

Jack walked back on board after finishing storing all the supplies, finding the Doctor awake curled up on one of the seats chewing his thumb in thought.

Jack sighed and attempted to ease the situation, “I told them not to wake you.”

He frowned, his voice wavering, “Oh did you now? Ease the pain of it all? They're going to be plugged back in.” He sat up staring to Jack raising his voice, “Why didn't you do anything?!”

“I tried, Doc, this is the only place we can go to get supplies. I can't just walk up to him and tell him to get out, plus they promised they wouldn't get put back.”

“You don't know that.” He curled back up in the chair in attempt to keep himself in emotional check.

“And you do?” Jack shook his head, “I have to trust them because they have to trust me not to EMP the whole damn city.”

“Now we don't have a medic.”

He sighed, “I know I tried. You're going to have to be careful now.”

“We can ask the Paternoster.”

Jack nodded, “I'll give them a signal when we leave but don't be wishful on it. We might not make it especially if they're too far off.”

The Doctor nodded, “Once we're back in can you run my simulation?”

Jack nodded patting his shoulder, “Of course.”

 

\------

 

The Doctor, as his younger form, sighed looking up to the twinkling starlight above him, it was ironic that he would resort to jacking in for comfort when he wanted the world to be a free place.

“My thief.”

He smirked turning slightly seeing Idris, with her wild hair and tattered dress walked up beside him, “Why do you insist to keep calling me that?”

“I am only stating the factual.”

“You forgot murderer, liar, old --”

She put a finger on his lips to quiet him, “No.”

He raised an eyebrow, talking through the pressure of her finger, “No?”

“No.” She showed a slight twinge of a smile bringing her finger down, “You are the Doctor and my thief, I choose the latter because that is what I knew of you first as.”

“I accept that because that's what I was doing, I had to save you from being decompiled.”

“I had gained a fault. It was the right thing to do.”

The Doctor laughed, “Emotion is not a fault.”

She tilted her head slightly confused, “I am not human, I am a program and it is a fault when it was never programmed into me.”

“You've had plenty of chances to reload yourself into the matrix.”

“I wanted to see how stealing felt. So I decided to steal you in return.”

He smirked with a slight chuckle, “So how does it feel?”

She cocked her head slightly trying to find the proper word, “Enjoyable.”

“Good.” He sighed and looked to her with a serious face, “Thoughts on Clara?”

“Belief that it would be a pointless venture as the subject only seemed interested in getting answers about non-relevant things, but --”

He smirked, “That's a first.”

She frowned at the interruption but continued, “But might be interested in the adventure.”

The Doctor nodded, “Sounds good.”

“But most unwise, there is no medic on board and Captain Jack --”

He chuckled looking up at the stars, “I'm the captain not him we just had to do that to appease everyone. Give them a little sense of control over me.” He sighed and looked back to her, “As for no medic it's my choice, I've had a good run. Getting far too old for this.”

Jacks voice suddenly blared out around them breaking the charade of them being surrounded by stars, “Hey did you want to talk to Clara? She's back.”

He grinned gently taking Idris hand kissing the back of it, “Another time.”

“Possibly.”

 

\------

 

Oswin: Hello

DrD1sc0: Why hello there. Straight off the bat with the private message.

Oswin: You were willing to answer my questions I thought you would be interesting to talk to.

DrD1sc0: Ah I'm not exactly boyfriend material.

Oswin: Who said I was looking for a boyfriend?

DrD1sc0: Sorry. A lot of people try to hook up on the internet, don't even know what the other person looks like and willing to get married and have kids right off the bat.

 

Jack made an audible groan giving away that he had been spying.

“JACK!” The Doctor shouted to him.

“Okay okay, I'll be in my bunk.”

 

Oswin: Seriously?

DrD1sc0: Boggles the mind.

Oswin: You're aging yourself there.

DrD1sc0: That a problem?

Oswin: Nope, just lets me know I'm not talking to kid.

DrD1sc0: Oh you would be surprised by some of these kids. Can have amazing philosophical conversation but once you add more than one into mix – well, you get the chat you had last night.

Oswin: As I said I'm a teacher I understand. Though I can just turn the chat off if I get frustrated, wish I could do that to my classroom sometimes.

DrD1sc0: Mind if I ask what you teach?

Oswin: English

DrD1sc0: So why is an English teacher so curious about a murderer?

Oswin: I don't think he is.

DrD1sc0: How so?

Oswin: Donna Noble, she came back and was fine.

DrD1sc0: She doesn't remember anything massive psychological trauma could do such a thing. Not a good basis for your theory.

 

The Doctor raised an eyebrow, a few minutes had passed and he hadn't gotten another response back yet. It was either a good sign or a bad sign.

 

Oswin: Sorry I had to think.

DrD1sc0: Oh thought I might have ran you off. What's your new theory?

Oswin: What kind of man would call himself the Doctor if he was a murderer?

 

He smiled, “Very clever.”

 

**Notes for the Chapter:**

> Hope everyone has been enjoying this :) hugs for the comments
> 
> FYI I am pulling some aspects from the game (Matrix Online) as well as it continued the matrix story as well. New Zion was made as they found out that machines weren't going to keep the peace forever and were eventually going to destroy zion and start anew as always.


	5. Chapter 5

A month had passed, Clara and the Doctor's 'DrD1sc0' had been conversing regularly, which ended up being Wednesday nights as Clara had accidentally missed some dates with Danny and late on markings which was not a good thing all around. She would always rush home which gained the notice of Danny, who would never get a plausible answer whenever he asked her what she was up to.

 

Oswin: Would you ever like to meet me?

DrD1sc0: I don't think that would be such a great idea. You really don't know me plus what would that boyfriend of yours think about you rushing off meeting a man you met on the internet?

Oswin: I can handle myself.

DrD1sc0: I'm sure you could but I would not like to risk it.

Oswin: We can meet in a public place.

DrD1sc0: Stupidest thing ever.

 

Clara was taken back, public places were always the best places for meeting strangers the more eyes on you. After a few minutes after thinking over she took a guess on why he responded in that manner.

 

DrD1sc0: I'm sorry that was stupid of me.

Oswin: You're either afraid of public places or that there could suddenly be too many agents, aren't you?

DrD1sc0: Which is one in the same if you think about it.

Oswin: I don't understand why you would have this fear of agents.

DrD1sc0: I told you, you really don't know me.

Oswin: Well I would like to get to know you.

DrD1sc0: What if I said it was a dangerous venture if you do?

 

Clara smiled, catching herself to which she questioned herself why, then decided to try something bold as her mind kept wandering to the question and she had to ask it, this man had to be him.

 

Oswin: Were you following me Doctor?

DrD1sc0: Only that night, I had to see what kept a person interested in a little website like mine for four hours.

 

Clara gasped, covering her mouth with her hands, she had been talking to the Doctor this whole time and it just was just a joke of a question that revealed the truth to her.

 

DrD1sc0: I will understand if you leave and don't come back, it's very much your choice.

Oswin: All those people are they okay?

DrD1sc0: Yes, very.

Oswin: What really happened with Donna?

DrD1sc0: The truth was all too much for her, started to have a mental breakdown so she had to be put back in with her memory wiped.

Oswin: Back in?

DrD1sc0: The matrix, what I had told you that first night it's all true Clara, you're living in a dream world my dear.

Oswin: I need to meet with you now.

DrD1sc0: We can't.

Oswin: Why not? You were in the restaurant why not now?

DrD1sc0: I unfortunately had to make a promise to meet those who wanted out. And out I mean out of the matrix desperately out that would mean leaving everyone behind and being another news story. I know you don't want.

Oswin: Why can't I just go out and come back?

DrD1sc0: It doesn't work like that.

Oswin: It sounds like it does because you do it.

DrD1sc0: I also have a bounty on my head. If you were to do the same, the system would mark you and people would start questioning the system because people know you and machines wouldn't want any of that and you would be killed and it would be blamed on me. You see why I want everyone free? No more endless murdering, no one a slave to a system and be a united world again.

 

Clara stared at the words, it was almost surreal what he was talking about but she had to understand it why he did the things he did and why this 'system' did what it did.

 

Oswin: Isn't there some way to show me?

DrD1sc0: Show you what?

Oswin: That I'm living in a dream world, in this Matrix and that you're not just a crazy man?

DrD1sc0: I'll answer that for another night, I believe it's getting late.

 

Clara looked over to the clock, time did indeed run short, though it seemed that it went by quite quickly than any other Wednesday and typed in her good night before closing the laptop. She hoped that that question could at least get her see him even if just once.

 

\------

 

“Hello Clara.”

The male voice came from the corner of her living room, making her pause as she had went to sit down and open her laptop like any other Wednesday. She looked over seeing the scrawny young man who was still in that hideous brown jacket standing in the corner of her living room grinning.

“How did you get in my flat?” She spoke with a slightly raised voice.

“Oh,” he reached into his jack pulling out a odd metallic object holding it out so she could see, “my screwdriver.”

“Doesn't look like a screwdriver.”

He shrugged, “Futuristic screwdriver. Though it just does little changes so I can get into locked buildings, hack into computers; Idris made it for me.”

“Idris?”

He smirked, “You'll meet her, get some good shoes on,” he looked to her outfit which was a jumper and skirt, “maybe pants too. We'll take your motorbike.”

 

The Doctor drove, at the frustration of Clara, the both of them to an industrial area that had been shut down and was slowly becoming one with nature as the vines and weeds took hold of the buildings. He pulled around near some of the dumpsters as to hide the bike and started too look around before taking his helmet off.

He turned extending his arms out to the building near by, “So here we are.”

Clara raised an eyebrow, “Yeah here we are. It's just a worn down building.” She soon jumped as Idris announced her presence by calling out the Doctor by his usual name she gave him. She turned and looked to the oddly dressed woman and could see they were a match made in heaven almost, “Thief?”

“She's not human, she's a program; an Intuitive Detection and Reporting System, and I saved her from getting decompiled by the system.”

Clara stared more at Idris in disbelief that she wasn't a human and then looked to the Doctor, “Decompiled?”

“My program was to be taken and broken back down into its source code, to remove the fault I had gained and then to be recompiled as new. My thief did not enjoy it even though it is necessary.”

Clara could hear the same drone in the voice like the agent in the video, “What was this fault?”

The Doctor grinned gaining Claras attention, “Emotion, but she's not what we're here for,” he pointed to the building, “what's inside here is what we're here for.” He looked to Idris, “Do your thing darling.”

“I already scanned before I made my presence known, system is at 10% alert level.”

Clara still looked utterly confused as the Doctor took her hand and walked her inside, “What does that all mean?”

“Sometimes there are glitches in the system, the system will know about it but will ignore it like an itch. Now the thing about Idris is, she was one of those alert programs, so it's really nice to have around so you can know that your starting to bug the system a little too much. Like a personal Geiger counter.”

Clara looked around as they walked through the building, looking back to see Idris following as well, before they stopped at a wide open area with the sun shining down through illuminating the floor. The Doctor leaned down collecting a few sizable rocks and handed them to her.

“Throw them in.”

Looking at the handful of rocks she looked back to him as he mimed to her to throw them into the light. After a few moments she threw a few in, gasping to the fact that they slowed way down as they made their way through the beams of sunlight before finally ending their trajectory through and returning to their normal speed. “What the hell?!”

He grinned watching her throw more rocks in, “Told you glitch in the system.”

“Can I jump in?”

The Doctor looked at the area of light for a while, “You might feel a little sick but yeah.”

Clara grinned as she ran as hard as she could jumping into the light, laughing as she watched herself slowly pass the area before exiting the other side stumbling.

“You alright?”

She continued to laugh, “Yeah I'm fine! That's amazing!”

Idris spoke up behind the Doctor, “Alert system at 20%.”

Clara jumped through again with Idris announcing another 10% jump, the Doctor caught Clara smirking, “Alright can't keep doing that much more. I'd rather not go above 50% with the system.”

She frowned, “That was fun though.”

“If you think that's fun, what about jumping across 100 yard gaps between buildings?”

“Can you do that?”

The Doctor nodded, “ You can too but I wouldn't suggest going and trying it. You're still in the system and they would very much stop you from continuing any further. This place will eventually be fixed as well.”

“What else can you do?”

“Oh a lot of things, since this is all just like a video game I know how to bend the system to my will. Things that are out of a superhero comic book.”

Clara nodded and looked around and then remembered the website, “So say you wanted to look like someone else?”

He grinned, “You remembered that part. Yes you can but thats a much much more advanced skill set,”

“Alert system at 60%.”

The Doctor quickly turned around looking at Idris with concern, “Whoa whoa it was at thirty what happened?”

“A male has entered. The soldier.”

He reached into his jacket pulling out an old looking cell phone hitting the speed dial, “Idris get out. Yeah, Jack emergency get Idris out. I should be fine.”

Clara watched Idris run off looking to the Doctor as he pocketed his phone, “What's going on?”

“Your boyfriend decided to follow you and he's bugged so the system went up a notch on alert status as soon as he entered the area.” He grabbed her hand leading them back out and finding Danny looking over the motorcycle.

“Danny what are you doing here?” Clara calmly shouted out to him.

Danny quickly stood up and turned around getting startled seeing a strange man holding hands with Clara, “What the hell are you doing with her?!”

 

**Notes for the Chapter:**

> Sorry for not posting yesterday I was a little blank on the story.


	6. Chapter 6

The Doctor looked at Danny for a moment before he realized he still had hold of Claras hand and quickly let go clasping his hands in front of him nervously, he was sure the system was in full alert now of his presence and he was just waiting for either one of them to turn into an agent any moment. “N-nothing.”

She looked at the Doctor noticing he was extremely nervous, “No it wasn't nothing. The Doctor was showing --”

“Clara!” The Doctor quickly turned grabbing hold of her shoulders, “No! Don't tell him anything, you can't tell him anything.”

“Why not?”

“Where is the program Mr Smith?” The voice of the agent droned behind them suddenly out of the blue.

Clara looked at the Doctor, who was blocking her way, squeezing at her shoulders having a look on his face that something bad was going to happen.

“Because that can happen Clara,” he let go and turned revealing the agent in Dannys place glaring towards the Doctor.

She stared and looked to the agent, “Where's Danny?”

“Where is the program Mr Smith?”

Clara raised her voice pointing her finger towards the man in the black suit, “No! You answer my question!”

“Clara he won't he's a bit of a one tracked mind. Danny is fine for now, agents can take over anyone jacked in at any moment but he can also be killed if I try to kill the program.” He looked towards the agent and glared, “She's already gone you should know that now so that's not the reason you're here.”

“You've eluded me for too long Mr Smith.”

He raised an eyebrow, agents never made it personal they were a system, “Do I detect a bit of anger? I think someone has developed a fault.”

“Almost 40 years Doctor.”

He chuckled, “Has it been that long?” He looked over to Clara, “Run, run back home. Don't ask questions, don't stop, just run.”

Clara looked between the two confused, “But what about Danny?”

“Run!”

Clara stared only for a moment before rushing off as fast as she could before slightly stumbling as what sounded like a small thunder clap happened behind her. Regaining her footing she turned around seeing that the building had started to crumble down, the fencing and weeds were hiding the very loud fighting that was sounding more like a vicious thunderstorm. Clara wanted to go back and watch but she decided to take the Doctors advice and run home.

 

Managing to run a decent way into town Clara caught a taxi right as what seemed like a stream of emergency services were making its way from where she had come from. The driver looked a little concerned looking into the mirror to look at Clara, “Hope everything is alright.”

Catching her breath she looked up, “What?”

“Whatever is going on, that's a lot of vehicles.”

She looked back, sadly not able to see as they had just turned a corner, “Yeah, I hope so.”

 

\------

 

There was nothing on the TV, radio or even the chat room though it had barely even been an hour since she got home. They were practically on the edge of town, no one could really see them but why were emergency services called? _Oh, no,_ the thought ran through her head wondering if the agent just called more backup if he even could. Clara sat on the sofa worrying about what happened and hoped both the Doctor and Danny were alright.

It was nearing almost midnight, Clara had started to phone Danny in hopes everything was over but the phone kept ringing and her heart sank with every call. She looked back to the chat room but nothing of importance till she noticed a new name in the list and also a new private message tab.

 

CapnJack: Where's the Doctor?

Oswin: I don't know what you mean.

CapnJack: Clara I lost track of him when I pulled Idris out, what happened?

Oswin: Who are you?

CapnJack: I don't have time to explain, Danny came by and everything went pear shaped what happened?

Oswin: He turned into one of those agent things and they started to fight. He made me run home.

Oswin: There was a lot of emergency vehicles heading that way too.

CapnJack: Shit. I need you to trust me and go into the bedroom. Whatever you hear DO NOT LEAVE till a woman tells you to.

Oswin: Okay.

 

Clara didn't know why he was suddenly following the directions of this new name but she felt that it was the right thing to do and she could finally make sure everyone was safe. She walked in and closed the door sitting on the bed, till she heard some odd noises come from her living room and a phone suddenly ringing with muffled voices speaking.

A soft knocking came to her door followed by a womans voice, “Clara?”

“Y-yes?”

“There's three people including myself in this flat with you, you may come out if you like.”

Clara slowly stood up and opened the door revealing a tall pale woman with black hair wearing a catsuit like outfit with a pair of swords to her side, she looked past to the other two a another female almost dressed the same and a short stocky bald headed man armed to the teeth with weapons and grenades.

“I am Vastra, behind me is my wife Jenny and our medic Strax. Please forgive him he get's a little carried away at times.”

Clara looked between all three in surprise, “How did you get into my flat?”

Vastra smiled, “Magic.”

Clara started to stammer as she was feeling now uncomfortable with these unknown people in her house and what she was getting herself into, “I-I don't know where the Doctor is.”

Vastra gently guided Clara out of her bedroom and into the living room, “I know dear, we don't either. We're hoping that he tries to get in contact with you.”

“Why me? What are you going to do with him?”

Vastra smiled softly, “He likes you, he never takes anyone to a glitch site. We're his friends we want to make sure he's safe.”

“What about Danny?”

“Danny?”

“My boyfriend an agent took him over,” she scrolled through pictures of her phone finding a selfie of the both of them holding it up to Vastra.

Strax laughed, “He finally got himself into a battle! I wish I could have been there to see it.”

A quick pound to the door startled everyone before Vastra started her slow move to the door with Strax not far behind. Looking through the peep hole she gasped, “It's him, Strax put the gun down.”

“It's a weapon madam and I intend to use it!”

“And you will kill the Doctor if you do and I will feed you to the squids!”

Strax grumbled, slinging the large weapon to himself as Clara peeked around the corner watching the both of them as they opened the door to a body falling over into their ready arms. She stepped back into the living room watching them haul the lifeless body to her sofa.

Clara smiled noticing it was the Doctor till Strax had moved away seeing a whole different face, it was old with silver locks to match. She looked over to Vastra, “Who is he? That's not him.”

Vastra smirked, “It very much is my dear.”

 


	7. Chapter 7

Clara sat on her coffee table staring towards the man laying on her couch, his clothes were torn from the fighting with some bruises and cuts covering his wrinkled face. She had stared at him till a cup of tea was placed into her view she took it and looked up to Vastra who had a light smile on her face.

“He didn't tell you he could change faces?”

Clara sighed looking back at him, “He did somewhat, I forgot. Is this what he really looks like?”

Vastra gently sat down beside her and nodded, “Though I think he's forgotten it himself, it was a slight shock when I saw him for the first time on the outside. I had always known him as a young face.”

“What's it like on the outside?”

She took a sip of her tea as she contemplated the answer, “It's something that you would question why any of us left and would fight for our freedom from a better place than this.”

Clara nodded watching him finally show some signs of movement, slightly mumbling to himself. He quickly sat up looking to the two women beside him his face growing sad as he stared at Clara.

Vastra smiled standing up putting her cup down in her place, “We should be going now you're awake.”

“Is Danny alright?” Clara looked at him longing for an answer.

He looked away quickly looking up to Vastra, “yes, please I think I'm done for a while.”

Vastra nodded, “Clara be a dear and go back into the other room please.”

Clara gently placed her hand on his arm which caused him to jerk back standing up with some uneasiness, “Clara please other room. You're still apart of the system and I don't know how much longer we have.”

“What about Dan-”

“He's dead Clara, since you're so desperate to know.” The phone started to ring and he picked it up, “Now go cry your eyes out so we can leave.”

Claras eyes went wide as she started to tear up, she wanted to slap him due to how heartless his answer was but lowered her head and walked out as she got the answer she was needing.

 

\------

 

The Doctor opened his eyes to the inside of the ship staying seated as his muscles were sore, he didn't remember it hurting this much the last time he had to fight but it had been ages ago. He looked over to the other three as they exited out of the system with Vastra getting up as soon as possible walking over to him.

“What the hell what that?” She furrowed her eyebrows at him, “what in creation made you tell her that in that tone?”

The Doctor sighed and slowly stood up, “We needed to go and she wanted an answer and trust me it would have been better than saying that I hurled her agent controlled boyfriend into an ambulance and then joked about the irony of it.” He started to step around as he was tired and didn't want anymore confrontation when a twinge of pain hit him and caused him to grab the chair.

Vastra stepped closer trying to put her hands onto him to help keep him standing, “Everything alright?”

He waved her away, “Sore, tired. I just need to lay down.”

“Strax can take a look --”

He furrowed his brow glaring, “I am fine, thank you.” He slowly made his way to his room.

Vastra looked over to Jack who had watched the whole thing, “Still doesn't liked to be touched?”

Jack shook head, “Though I could have sworn he had held her hand but the glitch in the area was making it difficult to see anything.”

“Should we try to extract her?”

Jack raised an eyebrow, “After what just happened? No. I don't even know if she'll keeping in touch anyway, you know how girls are.”

Vastra narrowed her eyes, “Yes, tell me.”

“S-sorry.”

“Anyway we should depart. Keep in touch?” She smiled towards him.

Jack grinned, “Always and I'll walk you out.”

 

\------

 

Clara laid in bed it had been months since the incident, no one knew what had happened which upset her more, she wanted to talk about it but she was concerned it would drawn unneeded attention to her. She had so much hate towards the Doctor for not being able to save Danny but she hated Danny almost the same, he would have still been alive if he didn't follow them. She was starting to understand why someone would leave this place especially if they knew some of the truth, knowing that one could become an agent and then die with the agent program still intact was unnerving. _Freedom_ , the word popped in her mind reminding her of what Vastra had said when she was asked about outside the matrix.

She grabbed her laptop pulling it into bed with her and opened the webpage with the chat up logging in.

 

Oswin (mibbit@2EF1383F.redacted) has joined the channel.

TacticalPlatypus: Hey look who it is.

5ush1Lazor: Damn I thought we were rid of them finally.

Oswin: Funny.

 

Clara looked at the name list and didn't see the Doctor or CapnJack online she frowned, something possibly happened to them.

 

Oswin: Has DrD1sc0 been around?

TacticalPlatypus: not been around since you disappeared too.

CapnJack (studmffn@AC743FF2.redacted) has joined the channel.

 

Clara was surprised the Jack appeared shortly after she did with him going straight into a private message.

 

CapnJack: Saying I haven't been able to get him out of his room since that night I hope you weren't wanting to talk to him.

CapnJack: Or yell or whatever you were wanting to do.

Oswin: How did you know I was online?

CapnJack: Idris monitors the room. Pretty much blew my ear drum out when you came in.

Oswin: I want out.

CapnJack: I hope it wouldn't be to take some sort of revenge on the Doctor.

Oswin: No. I made my peace with what happened but I still can't get over the fact that I'm pretty much someones play toy. I want out I want to be free.

CapnJack: Tomorrow evening wait out side your building, the Paternoster gang will meet with you.

Oswin: Paternoster gang?

CapnJack: Sorry Vastra, Jenny and Strax, you do remember them yes?

Oswin: Why isn't the Doctor going to do it?

CapnJack: It's just me and him Clara we always have them help, he's always been the decoy with the agents but since we haven't stirred too much trouble this should be a piece of cake.

CapnJack: Remember tomorrow. Don't pack anything because you won't be able to take it along anyway.

 

**Notes for the Chapter:**

> Thank you all for the comments! I get so worried when I post these.


	8. Chapter 8

Clara stood on the corner slightly away from the building of her flat, she couldn't believe what she was doing it felt surreal but to then think of the science fiction of life as she knew it being unreal was just the same. It felt like an eternity waiting but as a black SUV pulled up she felt it was finally worth the wait. The rear blackened window rolled down revealing Vastra sitting across the way, “Shall we?”

Clara nodded opening the door getting in seeing Jenny across from Vastra with Strax at the wheel as they pulled away. “Jack said the Doctor wouldn't be here to be a decoy why is that?”

Vastra smirked, “We're a little more rebellious than the others.”

Clara smirked with a slight confused look on her face, “What does that mean?”

“We're not to interfere with anyones knowledge of what they know. They have to have a hint that something is going on and they find it for themselves and then we're allowed to extract them quietly without fear.”

“So something like a video would be too much?”

Vastra nodded and grinned, “You should have seen the Doctors face after he came back with that, like a child getting the best Christmas present of his life.”

Clara laughed just but a little before looking out of the window watching the buildings and people pass by. “How has he been?”

“From what Jack has told me either hold up into his room or in his personal simulation. Between your boyfriend and Amy and Rory he's doesn't help anymore.”

Clara looked over to Vastra, “What happened with Amy and Rory? He said they were fine.”

“They are,” she sighed, “they punished him for releasing the video, new zion and the machines, by taking them into their care. They're safe.”

She grew with concern,“What are they going to do to me?”

“Nothing dear. You wanted out on your own, we're following the rules. They can't touch you.”

“They will be obliterated with acid if they dare touch you!” Strax shouted shaking his fist causing the three in the back to laugh.

Clara leaned over doing the best to whisper to Vastra, “What is wrong with him?”

“He was a military commander, one too many deployments to the front line. He's fine, really, we just have to keep his psychotic episodes in check.”

Clara's eyes went wide for a moment before the vehicle stopped near the abandoned building they were destined to go to. After stepping inside she was taken to what looked like it had been once an apartment that contained a desk, a few chairs and equipment set up around. Jenny pointed her to the chair to sit which she placed leads on her before Vastra spoke up.

“After this point Clara there is no going back, you can continue this or we can make you forget everything you ever experienced that was related to the matrix.”

Clara nodded, “Yes I'm ready.”

What happened next seemed all a blur after downing the red pill, visions of a surreal mechanical world, almost drowning and a bright light blinding her before standing in front of what seemed to be Vastra, her appearance less regal than before. “Hello, dear, you're safe now.”

 

\------

 

Clara smoothed her hand over the months growth of hair from her previously bald head, she wished someone would had mentioned this tiny detail but was happy that it was growing this fast. She had been tempted to ask about when she could visit the Doctor but somehow she felt it rude since the Paternoster crew was taking care of her getting her acclimated to her new life, plus she found it amusing to best Strax in hand to hand training.

Clara sighed at the 'breakfast' that was in front of her, another detail that was missed, with Jenny sitting beside her. “I'm amazed you hadn't asked to see the Doctor.”

Clara smirked, “Well I didn't know when it would have been okay to honestly.”

“We could see about right now. I know Jack has been missing the company.”

Clara smiled and nodded, “Yes, please. I've been wanting to meet Jack as well never got to meet him apart from the chat.”

“Wouldn't have been able to he's freeborn like the rest of our crew.”

“I figured that part out.”

 

 

Clara tried not to act like a child on Christmas day as the hovercraft set down, as she was both going to meet Jack and the Doctor but step outside the ship she had been holed up on for over a month. She was accompanied by Vastra and Jenny walking on the uneven ground of the maintenance tunnel towards the other ship.

Jack stood at the end of the ramp grinning at the three, “Ladies.”

Vastra smiled, “How have you been Jack?”

He sighed loudly, “desperate,” then chuckled, “sorry. I've been good, for being a babysitter.” He smiled to Clara, “Finally glad to meet you Clara. Welcome to the Tardis.”

She grinned and rushed up to him giving him a hug, which he automatically gave in return. “Thank you.”

Separating from the hug he looked down at her small form and smirked, “Thank you for what?”

“Uh, I don't know really. It felt like it should have been said.”

Jack smiled, “Anyway come on, he's been moping around in his simulation.”

 

 

The four walked inside, sadly she was hoping for some variance to all the hovercraft but found none apart from home made odds and ends strewn about both craft. Jack hopped into the seat in front of the monitors, Clara still hadn't mastered deciphering the text on the monitor but noticed one was golden in color.

“Jack what's with the gold color on that monitor?”

“That's Idris or more like that's how she looks in code.”

Jenny peered over looking to the other monitors, “He hasn't made a new look?”

Jack shook his head, “I think he's coming to terms with his age.”

Clara peered over the monitors to the Doctor laying in the seat plugged in, he seemed frailer than when she saw him in the matrix. She walked over studying his face, the paleness of his skin, the wrinkles that lay on top and the silver curls that adorned his head that hadn't seen a combing in ages.

Jenny gently tapped at Vastra and Jack to take their eyes off the monitors just in time to see Clara take the Doctors hand before noticing the Doctor in the simulation was looking at his hand like he could feel something.

“No way,” Jack said quietly, “we need to get her in there.”

 


	9. Chapter 9

Clara opened her eyes looking around, a heavy star field up above with clouds for the ground. It was interesting that was for sure but everyone had their favorite simulation. She carefully walked across the fluffy uneven 'ground' in the direction she was facing, Jack had put her out of the way to not startle him but still warned that he might be on the defensive. She started to see him seated in the clouds, practically wearing the same thing as he was wearing on the outside, the black holey sweater with black pants, staring up towards the stars softly mumbling to himself before turning his head and looking towards her.

“Who the hell are you?!”

She was taken back by the question and stopped in place watching him stand up, “Doctor, it's Clara.”

He laughed and looked up shouting, “Very fucking hilarious Jack. You should have coded Marilyn fuckin' Monroe for me if you thought I was that desperate.”

Clara frowned, “No Doctor, I'm really Clara. I'm seated right beside you on the Tardis.”

He shook his head still laughing, “Never told you the ships name. Good one Jack.”

Clara stepped forward, “Please come out of the simulation.”

He held his hand up to make her stay in her place, “No, you stop right there. You will not touch me and I will certainly not come out of here.”

“Doctor, I don't hate you for what you did.” Clara sighed as she watched him shake his head growing angrier.

_Tell him he held your hand._

Clara looked around to the voice who repeated the sentence and then looked to the Doctor, “You held my hand.”

He stopped and looked at her confused, “What?”

“The building with the light that let me float, you held my hand.”

He slowly stood up as he thought of all the possibilities of anyone knowing that apart from Idris, and then dismissing that Idris would play a horrible joke on him, “Why?”

“Why, what?”

“Why did you leave? You were safe, you had students to teach, you had a life.”

Clara nodded, “Had. I couldn't stop thinking of it all, that anyone could be an agent in a heart beat and then die and be discarded like waste.”

He frowned, “You could have just asked us to wipe your memories.”

She shook her head, “No, I enjoyed our conversations and I liked the glitch area. Those are memories I don't want to give up.” She stepped a bit closer smirking, “I'm also enjoying kicking Strax's ass.”

He started to laugh in surprise, “I bet that is something to see.”

She held out her hand, “Come on, Jack said you've been in here for a few days. Come out and see me.”

 

Jenny started to jump holding onto Jack while giggling as the three of them watched the Doctor take hold of Claras hand without caution before giving the signal to disconnect them.

“I can not believe it.” Vastra gawked at the monitor, “she did it.”

“Come on, love, let's get them out of there.” Jenny rushed over to the chairs to help pull the connection as soon as they came to.

As soon as they were awake and sitting up facing each other the other three made a small circle around them to watch. The Doctor was slightly hunched over nervously looking her over, “How long have you been out?”

“Over a month.”

He nodded, “Thought so because of your hair.”

Clara giggled, “I miss it.”

“Luckily it grows.” He softly smiled looking down to his feet.

Clara stood up walking over to him surprising him in a hug, his arms stretched out in an awkward pose unknown if he should try to run or what he should do next. What happened next surprised the onlookers as the Doctor finally put his arms around her reciprocating the hug.

“I am sorry for what I did.”

“You had to do it, it was no other way.”

“There's always another way Clara, sadly the agent never gave me the chance to.”

He broke off the hug looking around at the three, their eyes in surprise. He cleared his throat and looked towards Clara, “I take it you'll be going back to the Paternoster then?”

Clara smirked, “I was kind of hoping to stay here.”

He sheepishly looked down, “T-that would be up to the captain.”

Jack smirked, “Oh I'm the captain now?”

“For now, because I've been an ass.”

Jack grinned and looked to Clara, “Yes I would very much like to have you on board.”

 

\------

 

Clara had easily settled in to her new home, it was a nice change as the Paternoster was busy practically 24/7 while the only sound on the Tardis was a soothing hum of the engines core. Till one night Clara, who had been walking around the ship trying to fend off the sudden insomnia that had came over her, thought she had hear a soft sobbing coming from the Doctors room. She walked over noticing the door had been left open a crack, unknown if he always did or it was by accident or even purpose this night.

Walking in she saw him huddled facing the wall on the cot, heavily sobbing from the dream he was currently in. She knelt down slowly slicking back his hair, with a few slight flinches in response, slowly starting to calm him down as she softly whispered in his ear.

 

Clara woke up to realizing she had fallen asleep knelt on the cold metal floor which hurt as she stood up seeing Jack leaning against the door frame smirking. Clara looked sheepishly towards him as he motioned her out of the room as the Doctor was still asleep.

“You know it's been 20 years since anyone, apart from Idris, has been able to touch him?”

“What?”

Jack nodded, “After Rose he just clammed up, didn't let anyone touch him. I was going to get a tranq for him, since that's the only way one can deal with the nightmares, when I came back I saw you were there calming him down. He trusts you Clara for whatever reason, he lets you in.”

“What happened with Rose?”

“Zion found out the machines were going to make a move to break the peace treaty at any point of time and they wanted to protect New Zion as there was two ways directly there, they decided to lock it down there and then. Everyone was in a rush to get out, we were trying to rush to get her and the gates closed.” Jack sighed, “Can't even send messages there. We only get a message out saying that Zion is still there.”

Clara nodded and looked back into the room, “Will he be okay or should I go back in there?”

Jack smiled, “I'll let you trust your instincts.”

 

**Notes for the Chapter:**

> Thank you for the comments and kudos and those who're taking a chance reading this :)


	10. Chapter 10

Clara stepped off the ramp of the hovercraft, she was grateful to finally be somewhere other than the ship after another month and to finally see New Zion. She was slightly disappointed to how it was as the Doctor and Jack had talked about it being a bustling civilization to that equal to London or New York city but there were no buildings except for a central building in the center and one could easily see the housing was built into the walls of the earth. She looked back waiting for the Doctor and then looked to Jack who was walking away heading off the docks, “Isn't the Doctor coming?”

Jack shouted back, “He can't.”

“Why not?”

Jack stopped in his tracks turning to look at her, “They'll arrest him.”

Clara frowned, she had been hoping he could show her some of the sights but now she didn't want to leave him by himself. Jack smirked watching her look back and forth between him and the ship knowing all too well what she was thinking.

“There will be plenty of chances to see this place again, go on keep him company.”

“You don't need any help?” Clara smiled as Jack shook his head and rushed back searching for the Doctor. She was slightly worried when she couldn't find him till she heard a spark and a muffled shout of pain coming from the engine room. She rushed down seeing him sucking on his hand looking up in surprise that she was still on board the ship.

“C-Clara what are you doing? You should be seeing the sights.” He looked down at his hand which was reddened from the shock but luckily nothing major.

She frowned at him, “You didn't tell me that you couldn't leave the ship.”

He shrugged, “Wouldn't think that would have mattered besides I wanted to tinker in here anyway.” He shook his hand wincing a bit before placing a fake smile on his face, “Okay well getting shocked.”

She giggled slightly, “Happens a lot?”

He nodded, the tingling still staying around a bit longer than before, “Think I'm done for today she doesn't want to be tinkered with.”

Clara frowned walking up taking his hand and looking to the spot gently rubbing his hand, “Let me know if it hurts?”

“You don't have to do that, in fact you should be out seeing the city.”

She smirked, “I want to be here.”

He smirked in returned and grabbed her hand, “More like be with me, come on let's go.”

“Go where?”

“To see the city.”

Clara gasped stopping and tugging on him to stop, “But you'll get arrested I don't want that to happen.”

He grinned looking to her, “Between you and me, I've snuck out before just let me get my coat.”

 

 

Clara walked around with the Doctor in the market, he wasn't exactly hidden as he was pretty much the only person in a hoodie, that was practically screaming that he was trying to hide, but he wanted her to see the city regardless of the consequences.

“Doct-”

He quickly put his hand over her mouth, “Nope this is one time that I'm going to be adamant about my name not being said.”

“Well what is your 'real' name?”

“Basil.”

Clara laughed, “I hardly believe that, Basil Smith?”

He slightly furrowed his eyebrows, “Hey you asked.” He looked around trying to make sure no one had been rushing off but noticed a familiar face, “Come on I see someone I need to meet.”

Clara held on the best she could as he almost dragged her through the crowd of people before they stopped at two seemingly familiar people.

“Amelia Pond!” The Doctor joyously shouted out.

“Oh my god! I thought I wouldn't see you again!” she shouted out in surprise, “What are you doing here?”

“Taking Clara around,” he noticed something different of Amy, her stomach a little bigger than the last time he remember, “I see you're eating Rorys rations as well.”

Rory glared at him, “She's pregnant, I see things still escape you.”

Clara giggled as he saw the Doctor turned beat red and try to hide under his hoodie, “How long?”

Amy smiled, “Almost five months. I'm guessing you've only been out about 3?”

Clara nodded and looked around, “This is all interesting.”

“Not quite as cozy as the inside but I'm much happier.”

Rory looked around before noticing security guards pointing in their general direction, “I think we drew some attention.”

Amy looked to see what he was talking about and noticed security heading their way, “Talking isn't against the rules.”

The Doctor sighed and frowned, “No but me being outside the ship is.” He tried to turn around to run away from the guards before he bumped into the head security officer that was only two steps away.

“Doctor, you're under arrest.”

Clara shoved herself in between the two, “No, please don't. It's my fault I asked him to.”

“It doesn't matter miss, he knows the rules.”

“What are you going to do to him?”

“He'll be jailed and then placed before the council so they will decide his fate.”

The Doctor waved his hands in the air, “Oh yes let us let people in silly robes decide my fate.”

 

 

 

Jack walked into the cell area frowning at the Doctor who sat, his head hanging low, “What made you think about going out of the ship?”

He spoke softly, “I wanted to show Clara the city.”

Jack chuckled, “First person you let in in 20 years and she gets you killed.”

“No it was my fault.” The Doctor looked up looking around seeing no guards were around, “Did you hide Idris?”

Jack nodded, “Told Clara not to mention it either.”

The Doctor stood up and walked over to Jack holding out his hand, “Thank you for everything.”

He was surprised but took a firm grip of his hand in return, “Well I just hope this isn't the last time we do this.”

“Sadly I think it is.”

 


	11. Chapter 11

“Doctor, you have repeatedly violated our non-interference agreement with the machines, endangered the lives of you and your crew countless times to have your rank and ship stripped from you, disobeyed direct orders and numerous other crimes that would take us into the next year just to read.” The elder council member furrowed her brow giving him a glare, “What do you have to say for yourself?”

The Doctor chuckled as he stood in front of the council seated at a long table, “What do I have to say for myself? Maybe you should be asking that to yourselves, what's the point of being free when the rules are just as worse?”

“We are on the brink of war-”

“Oh please that's been used for thirty fucking years, they would have done it by now. From all the glitches and program faults I think they have more – ,” the Doctor stopped making a realization, there have been way too many glitches and faults in the system.

“The machines can handle that they have always handled it.”

“No, shut up!”

A male on the council stood up, “How dare you speak to the chair woman like that!”

The Doctor pointed to him, “You shut up too.” He turned to look to the audience finding Jack, “Jack, I need Idris. Don't question just get her.”

Jacks eyes went wide as he pulled on Clara as they left the council area, “Come on I'm gonna need your help.”

The chair woman looked to the Doctor with a raised eyebrow, “What are you doing?”

“Well apart from implicating myself in another crime, I'm going to prove why the machines hadn't decided to wipe us all out. They're too busy with their own problems.”

The still standing man looked at him in surprise, “You are not going to talk yourself out of this!”

“I told you to shut up and stay that way.” He grinned, “Oh and hope it doesn't take 2 hours for Jack to get her either it's a lot of heavy equipment.”

 

 

It was nearly an hour as Jack and Clara manage to return with boxes of equipment with a monitor streaming gold code down its screen on a dolly rolling it up beside the Doctor. Jack leaned over whispering, “You do know what you're doing right?”

He nodded while looking to the council and pointing to the equipment, “This is Idris or as the matrix calls her an Intuitive Detection and Reporting System, a program.”

All of the council stood up with the chair woman speaking up, “You stole a program from the matrix?!”

“And I stole him.” The speaker of Idris' voice replied.

The Doctor smirked and chuckled, “Yes, yes I did and the reason why I did was because she had developed a fault and was going to be deleted.”

“Decompiled.”

He shrugged, “Same difference.”

The councilman who had been vocal spoke up again, “If the machines found out -”

“Last time, SHUT UP!” He cleared his throat, “Idris how many years have I had you in my care?”

She started to drone her reply, “10 years, 3 months, 14 days -”

He smirked, “I only said years dear, you're going to break them.”

“Apologies, my thief.”

“So I've had her long enough that the machines practically don't care anymore.” He smirked, “From the last time you scanned the system, how many faults are?”

“1648 faults in a 35 year period, three times greater than the last cycles full 102 year period.”

The chair woman sighed, “what is the point of this?”

He sighed, “I've watched squids on the surface circle mindlessly, seen my fair share of glitches that lasted for a few years time before they even got fixed and even making an agent program very, very pissed off at me in fact is really the only thing in the matrix wanting Idris. They're breaking down because their little reboot didn't clear everything out.”

“If it was an issue they would have contacted us.”

He shrugged, “Maybe they didn't want you to know. Fear that we would take advantage of this little issue.”

The council man spoke up once more, “You realize that you're stating that they are scared? Machines scared?”

“Idris what emotions have you experienced?”

“Happiness, sadness, fear,” she paused for a moment, “and love.”

The Doctor paused before clearing his throat and moving on, “We need to help the machines and hope out of that we become united, end this war permanently.”

“You do realize, Doctor, that is impossible? They would deny every word of it and then destroy us because we know.”

He shrugged, “So find someone that they trust there has to be a good group out there they trust.”

After a few moments of quiet discussion the chair woman stood up looking to the Doctor, “At this time the trial for the charges upon you are suspended for another time pending your successful assistance with the machines problem and negotiation of ending the war. We expect monthly reports on your progress.”

The Doctor looked at then in shock but nodded and turned exiting out of the room with Clara and Jack soon following him with Idris. Clara gave him a confused look, “That's good right?”

He shook his head, “It's a death sentence. The machines want to kill me just as much as those idiots, who by the way if you didn't realized just made me the one to fix the problem.”

“So what are we going to do?”

“Run away.”

Jack sighed, “Now without a place to restock supplies.”

Clara looked to him, “We can fake the reports.”

The Doctor chuckled, “Then they would look for us because we aren't dead. We have to go to the machine city itself.”

Idris spoke up, “There is another way but it would be better to discuss on the Tardis.”

"Well you heard the lady let's go!"

 

**Notes for the Chapter:**

> I do hope that this makes sense as I had to rewrite it and took me a while to do so. My brain hurts hope yours doesn't.


	12. Chapter 12

**Notes for the Chapter:**

> now the reason this story is explicit.

The Doctor sat in his room his head in his hands realizing it would have been easier if he hadn't talked his way out of this because now he's going to be on the run and out here there are no other sanctuaries one can go to. He ignored the rapping on his door, he wanted to be alone to clear his thoughts from the day.

“Doctor?” Clara had opened the door peeking inside.

He sighed, “The point of me not answering a closed door is that I want to be left alone.”

She frowned, walking in regardless of what he spoke to her, “Do you always run away?”

He sat up looking to her, “There are reasons.”

She sat down beside him taking hold of his hand, “So what are we going to do?”

“You and Jack are going to go on the Paternoster and I,” he sighed, “I'm going away, it's what they want.”

“No, we're going to do what Idris suggested.”

“I'm not going to put Idris back in the matrix. What's the point of saving her to then get deleted in the end?”

Clara nodded, “I know you care for her but if it's the only chance to help them and then possibly get a true peace treaty that will lead into everyone co-existing happily, I will surely fight for it.”

He sighed and shook his head, “I don't want anyone else to die.”

“We all have to die sometime,” she leaned over and kissed him on the cheek, “it's late you should sleep.”

The Doctor nodded and hesitated before speaking, “W-would you stay here?” He started to stumble over his words like a nervous child, “I-I know I'm just a silly old man but I like you Clara, you make the nightmares go away.”

Clara grinned, “You don't have to woo me, though I think Jack will be disappointed.”

He chuckled, “No actually he won't, he has someone, Alfonso I think is his name.”

She laughed out loud for a moment, “I thought he was a big womanizer.”

“Anything tickles his fancy even Idris.”

“Bet that was interesting to see him try and hit on her.”

“She was very blunt in saying that their interfaces were not compatible with each other.”

Clara giggled, “So Doctor are our interfaces compatible?”

“That will be an answer for some other time,” he sighed, the tiredness was showing, “I haven't slept yet.”

Clara smiled softly, laying down on the cot against the wall with him following suit nestling his head against her shoulder taking her hand once more kissing the back of her fingers.

“Hey Doc –,” Jack walked in the left open door and stopped seeing the two in bed, “good for you.” He smiled as he walked back out closing the door leaving the two laughing for a moment.

 

 

Clara woke up to the Doctor gripping her hand tightly, he was on his back and Clara had been laying against him, gasping for breath in the nightmare he was having. She tried to free her hand from his grip but he only squeezed tighter, “Doctor, shhh, it's okay.”

“I-I don't want to die,” his breath shuddered as he struggled to inhale, “I don't want to die.”

Clara could only imagine what he was dreaming but at least she knew he could hear her. She shifted using her other hand to gently run it through the silver curls, “It's just a dream, shhh.”

“So scared.”

“I know, I know you're afraid, it's alright, it's alright to be afraid. “ His breathing was starting to calm, “We're going to face them and we're all going to be afraid and that's okay. “

He had stopped squeezing her hand and calmly laid there his breathing returning back to normal for a few minutes before softly speaking, “Thank you.”

“What were you dreaming of?”

“Re-living it is the more proper term.” He sighed finally opening his reddened eyes looking to her, “I was barely out of the matrix when the machines attempted to destroy Zion, I was told to help with the defense but I ran, I ran and I hid.”

“It's okay I'll be here always.” She caressed his cheek with him rolling to his side pulling her close to him, his hand wandering under her shirt feeling the softness of her skin mixed with the metal along her spine. They looked into each others eyes as they caressed each other before Clara leaned in closer just barely placing a kiss on his lips.

His hands had paused for a brief moment before squeezing at her skin as he kissed her back gently at first slowly starting to pulls small tastes of each other from their lips. He pulled at her shirt which she was very eager to comply with him following suit, embracing her close to him as the chill of air surrounded them.

Clara dug her nails into him pressing herself against his noticeable erection, “I want you.”

“Slowly,” he moaned softly, “body's never had sex before.”

“Talking about yours or mine?” Her hand slipped underneath the hem of his pants gently taking hold of his decently sized member in her small hand.

“Oh god,” he groaned his hips hitching up against her, “b-both.”

“Really?”

He nodded pushing down her pants as she did the same to him, “Was waiting for the right one.”

“Hope I don't disappoint.”

“Hope I don't either.”

He gently teased at her folds coaxing the wetness to flow from her core before he pressed his erection against her ever so slowly, closing his eyes concentrating, making sure he never hurt her. He opened his eyes gazing at her as she bit at her lip, unsure if she was okay. “I'm not hurting you am I?”

Clara shook her head, moving her hips slowly against him feeling the sensation of being so full, “It's fine, it's great.” She closed her eyes letting out a soft moan as the Doctor started to move inside her. She pushed against him managing to roll themselves over with her on top, watching his face gaze over her body as it slid against his cock.

His fingers grazed at her breasts, teasing her nipples harder, before his hands fully took the small mounds of flesh groping and squeezing at them as he groaned as her body squeezed him in response. Clara smirked leaning down to lay on top, his arms wrapping around her, as she laid her head down kissing at his collar bone. Their movements were slow and sensual, as if time had stilled, feeling every touch, movement and moaned breath of each other as the pleasure built between them.

The Doctor rolled them back over, her legs wrapping around his waist as he thrust into her harder as her moans grew louder. He groaned as she clenched around him, her orgasm pulsing, coaxing him on to release his seed inside her. He tried to hold back, how he wanted to feel it again to not let the night end but she had moved just right pulling him into her more with her legs that he buried himself deep within her pulsing with his own release. They laid together planting gentle kisses against their lips, as they both drifted to sleep.

 

 

Just before sleep took it's gentle hold, Doctor could have swore he heard Jacks muffled yell, “Fuck yeah!”

 


	13. Chapter 13

They realized the council didn't care about them after the first report they sent which at a glance looked like a professional report, till you actually read it and realized that it was a bunch of nonsense and hidden sentences mocking the council. The next month the Doctor didn't bother, which the Paternoster informed them that the council wanted the salvage of the ship to be returned. Of course, he was right, they wanted him dead luckily he had allies that would hide the fact he was still alive. Rations were going to be tight for a while but they would be able to make do.

 

 

The Doctor groaned as Clara ground her hips into him as he was strapped into the jump seat. She had figured out he was a virgin even though their first night together one would have never guessed but that was slightly thanks to Jack. It was beyond him why she wanted him to try new things, the bed was perfect but then again watching her naked form pleasure herself all while being at the mercy at her was an interesting thrill one that was sending him over the edge.

“Clara,” he panted shutting his eyes tight, “I'm, oh god, I'm gonna cum.”

He felt her lean forward, placing small kisses against his jaw, speaking softly with a hint of her wanting to moan, “cum for me.” He hitched his hips up, groaning as his arms now strained against the restraints wanting to wrap his arms around her. He tried all he could to hold off but the small mewling sounds she was starting to make coupled with her squeezing around him finally caused him to roughly thrust up as he came, with her loudly moaning pressing herself against him as she shuddered with the orgasm she had been building the whole time.

The Doctor finally opened his eyes after an unknown time looking at the ceiling of the hovercraft feeling Clara gently place kisses at his neck almost sucking at the skin. His arms still were restrained and he sighed, “Clara could I be released?”

She giggled, “I don't know I thought I could keep you like this and we could do it again.”

He groaned, “As much as I would love to, I would like to be let go getting uncomfortable.”

Clara smiled and kissed him on the lips before sliding off and undoing the restraints rubbing the reddened area of his arms, “Plus we kind have kept Jack in his room for a while now.”

The Doctor chuckled, “I'm actually amazed he didn't try to sneak out and watch us. I could have sworn the last few times he's made comments.”

Giggling as she put her clothes on, “I'll let him know.”

 

Jack grinned wildly as he came out looking to the Doctor who just barely got his pants on, “So do I expect a litter of children running around soon?” He chuckled a bit when the Doctor looked up in surprise, “You've been going at it like rabbits.”

He looked down for a moment and smirked, “Well I did catch the rabbit didn't I?”

Jack laughed and then sighed, “You know we can't keep running.”

The Doctor frowned as he reached down for his shirt, “You're free to leave at anytime.”

Jack pulled him over away from the open area of the ship and spoke in a hushed voice, “And what's going to happen when she leaves to? Or if she doesn't and has something happen to where you need New Zions help?” Jack shook his head as the Doctor fell silent looking away, “World doesn't work on hopes and dreams John.”

“Told you to never speak that name.”

“Yeah well right now you're not the Doctor, you're a coward. I'm willing to go to the end of the universe with you and die if it means we can stop running and fighting. I'm sure she is too.”

“I'll think about it.”

Jack pushed his finger into the Doctor chest, “Yeah you should think about it real soon too because we're going to be out of supplies before the Paternoster can attempt to give us anything and I'm more than willing to turn up again just so I don't starve to death.”

“I want to talk with Idris alone,” he sighed, “then I'll give you an answer.”

 

 

Clara had come back in seeing the Doctor laying back into the jumpseat and Jack at the monitors, “What's going on?”

“I had to push him into a decision,” Jack sighed, “and I know he's trying to talk Idris into another way.”

She frowned, “Why did you do that?”

“I just told him that we wouldn't be able to get supplies in time. ” He looked over to Clara, “He doesn't know the truth of it all, the council knows we're still alive and they've recalled every ship that's out so they can't help us.”

Clara nodded, “How long is he going to be in there?”

Jack shrugs, “Depends on how the conversation goes.”

She patted his shoulder, “I'll be in bed then.”

“It would be best.”

 

Clara woke up to the Doctor having fallen asleep at the small desk and chair that was inside the room, head buried into the crook of his arm, she was surprised that he didn't get into bed. Walking over she gently rubbed at his arm, softly speaking him to rouse him out of an uncomfortable sleep. Smiling as he finally shifted turning his head so he could peek out, “Come to bed.”

“I didn't want to wake you,” he sleepily slurred as he sat up.

“Do you think that matters?” Clara giggled a little wiping the small spot of drool off his face as he worked himself into a position to shift himself over to the bed. She climbed into bed after he settled himself in her head laying on his chest hearing the what had been a nervous thump of his heart calm down.

“You're beautiful, do you know that?”

Clara sighed, she figured that the conversation did not go as intended and he made up his mind that he would sacrifice himself, “My hair has still has a ways to go.”

“It doesn't matter to me.” He yawned putting his arm around her giving her a gentle squeeze, “stay with me for a while?”

“As long as I can.”

 


	14. Chapter 14

Clara groaned as she was woken up by the Doctor they had, for almost a week, been running around the matrix cashing in the favors people and programs alike had owed the Doctor in preparation for what they were planning to do, she was tired from practically no sleep and hardly any food because she was too tired to eat. This time was no different as the massive headache and nausea was forming making her cling to the bed as he tried to pull at her. “Doctor, no.”

“We need to go this is the only time he will see us Clara!” The Doctor tugged more till he successfully pulled her up which had a reply of her slapping him, hard, across the face.

“I said no!” Tears were starting well into her eyes, “A week we've been at this! You said we were done yesterday and here you are waking me up after, what an hour?”

He spoke softly feeling the redness of his face,“It must have been a couple hours.”

Clara grunted in frustration, gathering all the strength she could so she could stand and walk out of the room much to the Doctors delight till he watched her turn towards the other rooms and walked into her old room.

“Clara what are you doing?”

“Telling you I'm done.” She leaned against the wall looking paler, “I can not function like this and if you're just wanting me there just to appease him like some trophy wife then you can forget about it.”

He stood there for a moment with his mouth slightly agape, “B-but I thought –“

“You thought what?” She groaned closing her eyes as the migraine pulsed in her head, “I have limits and I know Jack does too and my body is saying sleep. How the hell you're still standing amazes me.”

“I-I don't sleep much, even with you helping with the nightmares, my body is used to it.” He frowned hanging his head bringing up his thumb to chew at in thought for a few moments, glancing up at Clara trying to keep herself standing, “You know what you're right. The last time I tried to talk to that pompous program I told him to suck my dick, in French.”

Clara weakly smiled, “So a break?”

He looked up nodding, “Can you walk back to the room?” She shook her head her eyes finally closing as he walked over and picked her up the best her could carrying her back. “Change of plans Jack; I don't care where we are right now we need a break.”

Jack was in shock as he heard and saw most of it, not that it was surprising he had dealt with the Doctor for most of his life and the one to two week stints of hardly any sleep was not new to him. After shutting down the system and getting some supplies he walked into the room looking at the Doctor who was sitting in bed with Claras head in his lap sleeping quietly. “I brought some things just in case.”

He was staring at her intently before speaking quietly, “I didn't realize it had been a week.” He looked up at him, “Do I do this a lot?”

Jack nodded, “I never complained since I can take power naps while Idris watched out for me. There are times you stay switched on I thought with her here that wouldn't happen. I tried telling you that she needed sleep but you were ignoring me.”

He looked back down towards his lap, his hand gently caressing her head, “I messed up didn't I?”

Jack smirked, “Yeah, I'm going to move the Tardis. Get some sleep.”

 

\------

 

Clara woke up to feeling something being pulled from her arm, a feeling she was sure she had felt before which was confirmed as she opened her eyes slowly seeing the Doctor replacing the IV needle in the port on her arm. He looked at her giving her a soft saddened smile kissing the back of her hand before putting her arm down, “Go back to sleep if you need to.”

“How long was I out?” It came out weak she took a guess as the small dull pain of her body waking up it must had been a while.

He sat down on the chair, “Um, a day, I think. Day and a half.” He sighed, “I'm an idiot.” Clara nodded slowly in reply with him looking sadder at her, “I can't guarantee that I won't do it again but I will try.”

“Have you slept yet?”

He shook his head, “I kept watch, make sure you were okay especially after you not waking up so I had to give you something.”

Her voice was finally getting normal when she spoke, “I think I'll be fine.”

“No,” he spoke the word sternly, “I'm not going to lose anymore.” He looked uneasy in the chair, if something like this had happened before or the fact that he didn't want to lose her as well. “I'll be fine, just get better.”

Clara tried to shift but her body was sore, as she was possibly in the same position while she slept, “In the bed please. I'll be better.”

Nodding reluctantly he helped her into a different position in the bed taking his place beside her as she laid her head on him like many nights before. He sadly still wasn't going to sleep, the both of them knew it, but it made the both of them feel better in their own special way. “Trophy wife?”

Clara made a small weak laugh, “Did I say that?”

“Yes about how I wanted you there to appease him, what gave you that idea?”

“I just felt like I was there as decoration sometimes.”

He gently ran his hand over her back, “No, no. You aren't. It's hard to describe but you're not that. Plus saying you can kick Strax's butt in hand to hand I need someone to protect me.”

“But you dealt with that agent.”

“He had a fault gave me the advantage.” He sighed, “I would rather not want to bring that up again either.”

“Sorry.”

“I'm sorry as well.”

 

**Notes for the Chapter:**

> next chapter might be a bit as i've hit a little mental block called Overwatch I have to deal with shouldn't be too long of a wait.


	15. Chapter 15

**Notes for the Chapter:**

> In the words of Gune from Titan A.E. "I've finished my nap!"
> 
> This one was actually a tough one to figure out but I did it!

Clara peeked out of a random room looking around to see if anyone was nearby or watching, while she had made a full recovery she still had moments of illness that required her to sneak away. Today was the day they were going to attempt to fix the problem, restart the matrix and bring another bit of peace to the whole. Seeing the coast was clear she walked out of the room back into the main area, the Doctor was already connected and inside, she looked over to Jack that was giving her a concerning look. “I'm fine just nervous had to calm down.”

Jack smirked, “You and me both. Ready?” Clara smiled and nodded getting into the seat, with Jack connecting her to the system. “Some reason Idris wanted to talk to you before you went completely in. Doctor knows but he wants you two to be brief.”

Clara was surprised but was curious on what she would want to talk to her about. After her senses came back to her she opened her eyes staring directly at a very close Idris who was curiously looking at Clara. “Jack can not see nor hear this conversation.”

Clara stepped back startled, “Don't know why he shouldn't.”

“You will understand when I am finished with our conversation.”

“O-kay?”

She held her arms down by her sides as she started her statement, “The Doctor has been one of the most interesting humans to be in contact with. In my time with him I came to understand and learn why programs wanted to be free of the linear logical thought of the matrix. They wanted to enjoy their happiness, sadness and love of things; the same emotions I have come embrace.”

She cocked her head in confusion, “Why are you telling me this now?”

“Because if you go it would end in sadness. I must take your place and rejoin the matrix; correct the logical thought.”

“He'll still be upset if you do that.”

Idris softly smiled, “For a time yes but there will be happiness again by something that will take my place.” She held out her hand towards Clara, “Take my hand.”

Clara was a little confused but with her adamant about taking her place she had to trust what Idris was saying. She took her hand which caused an immediate wave of warmth flow over her blurring her vision before the feeling disappeared seeing herself standing before her.

Her double smiled, “Take care of them.”

“ _Uh, what's going on? Why are there two of you?”_ Jacks voice came out of the blue.

The Idris Clara smirked, “Upload me Jack and disconnect Clara. Don't let the Doctor know alright?”

“ _I'm going to miss you.”_

“The same, I enjoyed your attempts to seduce me they were quite interesting.”

“ _Shame you never gave in.”_

“My heart is for someone else.”

 

\------

 

The Doctor was getting a little anxious, he knew Idris could get a little long winded in the conversation whatever it had been about, but time was important as the window was closing. After pacing for a few moment he saw the glint of green light flash turning him around seeing Clara before him. “Hopefully she didn't talk your ears off.”

She smiled, “No she had forgotten to give you a key.”

He raised an eyebrow, it was very unusual for her to forget things as she was the one usually to remind him even if he had never forgotten. “So where's the key?”

“Not physical had to be imprinted onto one of us.”

“More like trusting you with it more than me.”

Clara shrugged, “You know her better than I do.”

The Doctor smiled taking her hand leading her out of the apartment to the waiting car outside and got in. “How are you feeling?”

“Nervous.”

He sighed rubbing his fingers against her hand, “Is that what you're really feeling or just what Clara would say?”

“What?”

“You know I could tell the difference between a human and a program yet you let me touch you. Idris why are you trying to trick me?”

Idris sighed as she went back to her original form, “There is no other alternative, I did not want to bring Clara to harm.”

He started the car and drove off, there was no time to waste anymore so he had to take her with him,“She is very capable of handling herself.”

She shook her head, “Not against an agent. Not against one that very much wants me back.”

“The system wants you back and that's a very determined agent.”

She smirked looking out the front window of the vehicle, “Because he loves me.”

The Doctor almost stopped the car with the statement but continued on looking over to Idris with a very confused look on his face, “What?”

“Systems like myself work in tandem with agents to scout out possible dangers, faults and glitches and we worked with each other till we started to love each other. I feared for our lives and hid his fault from the system. It is why I let you take me as I could not hide mine, I was closer with the system and it would have found out.”

“But he doesn't know that.”

She nodded, “As it should be it is so he wouldn't be found out either, my thief, but we are the reason why the system is failing. We have to go back.”

He huffed, shifting uneasy in the seat as he drove, “You just made me waste all the favors I had.”

“We still potentially need them. The agent is still angry,” she sighed, “it is why I kept Clara away.”

The Doctor nodded, “Better than loosing both.”

“Three.”

“Three? What do you mean by that?”

Idris looked directly at him and stated matter-of-factly, “If you were to lose Clara you would also lose the anomaly inside of her.”

He pulled the car over rough and stop it, the seat belts locking into place holding them back. He sat staring out the window wrapping it around his head what she had just said, “She's pregnant?”

“If that is what you call her condition of excess code is described as then yes.”

 

 


	16. Chapter 16

Jack looked over to Clara, he had been reading their lips watching the conversation unfold in front of his eyes, it wasn't really a surprise that it would eventually happen but that it was a surprise that Idris knew if it was even at all true. Clara walked around to him looking towards the monitors confused why the car had stopped and then looked to Jack looking up to her. “Why is the car stopped?”

Jack closed his slightly opened mouth and cleared his throat, “How long has those nerves been hitting you?”

Clara nervously laughed, “Just today why?”

Jack paused for a moment, he couldn't just say it outright maybe she didn't realize that she was. “Idris didn't say something to give you a hint of something going on with you?”

“Wait what's going on with me?”

“There are, um,” he cleared his throat again, “tests in the med bay.” He looked at Clara who was initially confused till the realization of what he was implying finally kicked in.

Clara spoke softly like she was embarrassed about it, “Oh, god I thought she was just adamant of me not going. I had been feeling like crap ever since that week I just thought I was just still sick from what happened.”

Jack smiled, “It's alright, you know you could have said something especially if it really was something serious.”

Clara sighed, “I know that but he was just so into finishing this and I didn't want to pause it all again but it sounded like something was going to happen, something bad.”

He nodded, “Doesn't take an intuitive system to know that, it's why he got all those programs.”

“Yet he doesn't take a gun.”

He laughed, “You haven't seen him fight.”

“You're right I haven't. I only heard it, sounded like a giant thunderstorm was going on.”

 

\------

 

“We need to continue our travel to the point.” Idris looked at the Doctor slightly confused as to why he looked suddenly scared. “What is wrong?”

“I um,” he nervously laughed, “never thought something like that would happen.”

“Humans are confusing, sexual acts leads to pregnancy yet you are surprised when it happens.”

The Doctor laughed again starting the car back on its journey once more, “Well I'm an idiot, I thought nothing would happen out of it. I'm old Idris.” He sighed tightening his grip onto the steering wheel with realization, “And I'm going into the hornets nest and to my death leaving behind people that will never know me.”

“You will not die, Jack and I have been re-configuring the emergency disconnect program for you.”

He gave her a sad smile, “Lets hope it works because I know there are no ships out there and we're too far from New Zion.”

 

They finally arrived at their destination, an office building near the middle of the city, with a small group of people in front standing and waiting. They both got out with the Doctor nodded to the group as they entered the building greeted by a security guard at a desk. It seemed like a normal person till he flickered, unknown if he had a fault on his own or it was caused by the corruption in the matrix itself.

“Offices are closed,” the guard droned looking angrily at the group.

“We have a key.” Idris replied.

“Offices are closed.” The guard repeated with another flicker.

The Doctor looked to Idris with a slight concern, “I take it he's not supposed to do that?”

“No he would be letting us in,” she walked around to behind the desk carefully, the guard repeating the same line not moving the bottom half of his body missing with pieces of matrix code visibly dripping from him, and stared at the monitors and buttons on the desk.

“Is that smart to do?”

“He is in a loop fault has been for some time his code is degrading from the damage.” She pressed the proper combination of buttons to remove the hidden security from the elevator and looked to the Doctor and the group. “It is recommended for the others to stay here.”

The Doctor turned to the small group, some looked like they were out of various goth punk bands or down to a modern day werewolf vampire film, “As I said before I have no clue what is going to happen but you won't owe me anything after this.” He looked to all of them nodding before turning back to Idris who was holding out her hand.

“Time to put me back Doctor.”

He nodded gently taking her hand as they walked to the elevator noticing her pulling out an oddly shaped key, “I thought you said the key wasn't physical?”

“I partially lied.”

He smirked watching her slot and turn the key opening up the elevator doors to a pure white room. “I hope I hadn't corrupted you too much?” They stepped into the elevator room with a silver elevator button which the Doctor was about to push when Idris stopped him.

“This is where the key is not physical as it is apart of my code. If you were to have touched it the emergency program would not have been able to save you.”

The Doctors eyes went wide, “Is it safe for me to even go with you?”

“It follows the rules of the matrix so I see no issue of you spontaneously dying but you will be the first human to be inside this area. I am unsure of what will transcribe.”

“Great you hope.” He sighed out of worry and hope Jack was watching them, “Jack tell her I love her and take care of her.”

 

\------

 

Clara looked to Jack as she watched on the monitors the elevator doors closed and their whereabouts in the system vanished from view, “Jack what did he say? I know he was talking to you.”

Jack sighed, “He says that he loves you.”

Clara began to worry, she had watched enough movies to know when that phrase was uttered something bad would happen, “Nothings going to happen right?”

He shook his head after a moments pause of trying to figure out what to say, “I don't know Clara. I-I really don't know.”

 

**Notes for the Chapter:**

> For some reason this chapter and the one before it were difficult to write but we're pushing on!


	17. Chapter 17

The Doctor leaned against the wall of the elevator as the disorientation he experienced was surreal, he couldn't tell where the elevator was heading. Idris looked over to him seemingly unaffected by it walking over and placing her hand on his chest. “I apologize I failed to expect any security protocols by your presence.”

“It's alright,” speaking was proving to be difficult as well, “how long is this ride going to take?”

“Two more minutes. Will you be alright?”

“I hope so,” he took hold of her hand in comfort, “as long as it ends once we leave.”

“I can not guarantee that as we are entering the source, it does not follow the rules and can control the matrix like the one anomaly.”

The Doctor groaned, that was something that totally passed his mind but of course things hadn't gone to plan, “Of course it does.” He finally found relief and the sense of the elevator slowing as it reached it destination with the doors opening revealing a large room of code with larger than life figure in golden code hovering in the center.

 

The robotic voice boomed, “Why have you brought a human here it is forbidden.”

Idris replied calmly as they stepped out of the elevator that shut after them, “I am here to return and be decompiled.”

“Your ability to do this task did not require human assistance.”

The Doctor stepped forward a few steps before realizing the floor was solid black which made it seem like an endless abyss below them, he looked up to the Source before he shouted slightly towards it, “I'm here because I know of your little problem.”

“We do not have a problem.” The golden coded body flickered like the guard before.

“Well saying your security guard is half gone, in a repeating loop and you look a little flickery, you do need my help.” He pointed to the source, “I want to help you if you help me.”

“Me equals to the human infestation occupying Zion and the illegal New Zion colony. Correct?”

The Doctor swallowed, it wasn't them knowing about the settlements it was that they understood what the Doctor wanted, “Y-yes.”

“We require the destruction of the current infection for a proper cycle restart.”

He frowned, “Now that's a problem.”

“For an animalistic species to hate one of its own we do not understand why you would have a problem.”

The Doctor chuckled, “Yes they would rather see me dead then to let me stand here talking to you but I have a lot to live for, especially now.”

“Love.”

“I doubt you know the meaning.”

The Source looked around the room in front of him with screens popping up starting to quick list the various dictionary based definitions of love before the Doctor groaned in protest.

“Ugh, you don't know the true meaning of love.”

It looked down towards him, “Inquiry: Do you?”

He smirked extending his arms out looking around him, “Well I'm standing here aren't I?”

The golden form leaned over in curiosity, “Explain.”

“Standing here in front of the machine core willing to die if it means we could have a life without fear.” He walked a few cautious steps closer still unknown if it was 'floor' beneath him, “I know you know what fear is, you experienced it when you found out about the New Zion colony. You were afraid that we would fly up to Zero One and take you all out. It's how this whole thing started, fear of not wanting to die. I want to end it to protect everyone I love; human, program and machine alike. All because they want to keep their emotions and their lives.”

“The human infestation will attempt to over power us and will fail.”

He held a finger up to his lips in contemplation and to mime to the giant glowing machine before him to shut up before bringing his hand down, “I know I'm only speaking words that will most likely be null later down the generations because someone got scared again but we can work together to rebuild the planet and get rid of that cloud, which I'm pretty sure you have figured out on how to get rid of.” The Doctor sighed, “It's why I'm letting Idris return herself, why I'm standing here knowing full well what you can do to me. To hopefully be the first one to say, we're sorry. That I am sorry.”

The Source glared at him before standing fully upright towering over the two, “Connecting to New Zion.”

The male voice replied, _“This is the envoy to the council.”_

The Doctor was stunned but not completely surprised that the machines had called directly into new zion and to a person he very much knew.

“The human known as the Doctor wishes to discuss a proposal.”

“ _The Doctor is dead.”_

The Doctor smirked, “Oh I'm very much alive, the council knows this Alfonso.”

“ _D-doctor?”_

“Yes anyway I don't have much time as I have a large machine towering over me. They're willing to renegotiate the treaty for real this time. We all live as one happy family.”

Another familiar voice spoke up which sounded quite like the very vocal councilman, “ _preposterous.”_

“Oh boy you. Didn't fucking think I could do it?” He looked up to the Source, “Hey if I give you this shit head will that do as a suitable sacrifice? I mean he's one of the ones that don't care and would rather nuke you from orbit if we could.”

“ _How dare you.”_

The Doctor was amused and pointed to himself even though the councilman could not see him, “Fuckin' dare I? I'd like you to stand here where I'm standing.”

“ _You know I can't.”_

“That's right because you were born of Zion, not of the matrix, so that gives you the right to be an asshole and think you know better. I do what I do because it has to be done. We can not sit here at a stand off while both sides waste away because we're scared.”

The councilman started to stutter as a female voice spoke inaudible in the background, _“Madam council please no.”_

The chair woman shouted loudly unknown if it was to the Doctor or to the council man but the Doctor let it play out, _“How dare you!”_

“ _This is a military matter ma'am.”_

“ _I wondered why the patrol reports from the Tardis were a little too formal. You are dismissed stripped of your authority and quite frankly if it wouldn't get me removed from my seat as well I would have you banished to the surface.”_

The Doctor chuckled softly, “Oh boy.”

The woman huffed and then calmly spoke, _“Doctor is this a legitimate claim?”_

The source once again spoke, “Explanation of the early failure of this matrix cycle; emotion was imported into the code. The system is failing as we attempt to compensate.”

Idris finally spoke up once again, having watched the interesting turn of events that occurred, “Which is why it needs me, I have come to learn and understand these emotions which can balance the system.”

“ _I thought you already had emotion? I know of some programs even that temporary liaison you had had emotion.”_

“Programs that display emotion have it programmed into them, this new occurrence of emotion is self-forming alerting the system to a fault. It has been decompiling programs that it does not need to and they are revolting.”

The Doctor softly spoke but just loud enough that it could be heard, “I would also like all those stupid charges dropped.” He sighed, “Please.”

There was a lingering moment of pause before she replied, _“Agreed.”_

“Permission for system stabilization before discussion of truce.”

“ _Yes of course. It will give the Doctor time to return to New Zion as well so he can help.”_

“Agreed. Connection ending.” The Source looked down upon the Doctor once more, “exit.”

He nodded looking over to Idris who had a sad smile on her face, “Will I see you again?”

She shook her head, “Probability of such a chance is null.”

The Doctor chuckled gently taking her hand kissing her knuckles gently, “here is to that null chance.” He sighed staring at her for a few moments before he turned and walked back into the elevator that had opened its doors once again. As the doors closed he watched as her form became golden code and started to swirl into the giant form.

“Decompiling code.” The voice boomed right as the doors closed.

 

The Doctor sighed looking down at his feet, the elevator was not giving him a disorienting sensation anymore and could feel that it was going upwards at a rapid pace. He started to smile as everything that had happened was finally filtering in, he had assisted in fixing the matrix and, hopefully, a tried and true peace treaty with the machines. He felt the elevator stop and looked up as the doors opened revealing a very angry agent with his pistol pointing at him.

“You killed her!” He yelled as the trigger was pulled and everything went black.

 


	18. Chapter 18

His senses slowly came back to him, he could tell it was bright around him and the floor he was on was smooth and cold but so far nothing else. He was either in limbo or well it couldn't really be heaven because after all the things he's done he never thought he deserved to be there. The ringing in his ears signaled that his hearing was finally returning as he could hear Jack yelling his name.

“Yes, god, I'm here.” He finally opened his eyes to the white room of the loading area construct, “what happened?”

“ _What do you mean what happened? What's the last thing you remember?”_

“Coming out of an elevator and figuratively shitting my pants.” He groaned as he sat up, his body was tingling revealing the soreness, “I take it that was the emergency jack-out?”

“ _Yes but you were out for about thirty minutes, I can probably fix that.”_

“No, no leave it. It works, did the matrix restart?”

“ _Yes right after a giant hand took care of that agent that was quite startled you had just suddenly disappeared. It's still down.”_

“Let me out and take us home.”

“ _Home? They're gonna let us in?”_

He started to seem agitated, “Yes and I got that asshole councilman fired too.”

“ _I wish I could have heard that.”_

The Doctor shouted, “Jack, out!”

“ _Right sorry.”_

 

The Doctor opened his eyes once again see Claras face directly hovering over him. As soon as the connector was pulled he sat up pulling her towards him burying his face into her shoulder softly sobbing. He could hear Jack say something but it didn't register as the feeling of her against him was all that mattered at that moment.

Clara softly ran her hands over his back comforting him, “Hey it's okay.”

“I was so scared, so, so, scared.”

“I know I was too after Jack told me that you said that you loved me.” Clara chuckled, “It was something I already knew.”

He spoke softly. “N-no it was when that agent was standing in front of me. It's true what they say life flashing before your eyes.”

Clara softly soothed him finally feeling him start to relax and slump into her as her normal comforting touches were working their magic against him, “Want to lay down?”

He shook his head, his body trembling, “Don't want to let you go.”

“Just for a moment then you can keep hold of me,” she kissed at the side of his head, “okay?” She looked up to Jack, with a guilty look on his face, walked around from behind them as the Doctor started to lean into her falling asleep.

“This is what happened last time, something in the emergency program just loops the fear he experiences right before it kicks him out.” Jack sighed looking down at the empty syringe in his hands, “Luckily this time he had you to keep him focused on something while I knocked him out.”

“What happened before?”

“He ran off and hid, almost couldn't find him before he,” he cleared his throat, “was almost scared to death in a very literal sense. ”

Clara frowned, “Will he be alright?”

“Yes since we can actually go to New Zion now.” Jack walked over and picked the Doctors unconscious form up taking him to a room void of anything except a bed and laid him down with Clara curiously following.

“You think that's alright, what happens if he wakes up?”

Jack looked to Clara and then back to the Doctor, “I don't know how he's going to be when he wakes up, though you're right he's gained such a resistance to the meds he might wake up. It's a six hour trip.”

She smirked, “I'll be alright.”

 

 

Clara had walked around to stretch her legs after sitting cross legged for nearly four hours to which she walked back in the room to find that the Doctor had indeed woken up and had curled himself into the far corner rocking himself in comfort. She slowly walked up to him crouching down a small distance away speaking softly trying to get his attention.

The Doctor spoke softly, “He didn't have to drug me.”

She slid over and sat beside him, “You weren't letting me go and Jack thought you were having an anxiety attack.”

He leaned against her and shrugged, “Maybe I don't know.”

She pulled him down laying his head onto her lap noticing his nose had been and still was bleeding, “Um, you're bleeding.”

He sighed, “I-I know.”

“Is that something to be worried about?”

“How long till we get home?”

“Like two hours.”

He spoke a little bit more softly this time, “No it's nothing to worry about then.”

Clara frowned, Jack had told her a very quick explanation on how the emergency jack-out worked so she figured out something was not right. “How serious is it?”

“What were you thinking of naming the baby?”

Of course he was going to dodge the question, better to think about other things. She smiled softly running her hand gently over his hair caressing him, “It's early to think about that, don't even know what it's going to be.”

“Never, never too early.”

Her eyes started to well with tears and she softly spoke, “What are you hoping it to be? Boy or girl?”

He closed his eyes smiling thinking for a moment before answering, “Girls, I want a lot of girls. So-so I could terrorize their boyfriends.”

Clara giggled through the tears, “Should have at least one son, name him Basil.”

He weakly smirked, he knew she meant a son named after him, “John.”

“What?”

“That's my real name.”

She smirked, “Why did you tell me Basil?”

“John is so bland.”

She leaned down placing a kiss on his temple before whispering, “Name one of our daughters Idris?”

“Yes,” he drew out the reply as his breathing slowed.

“Please don't go.”

“I'm not going anywhere.”

 

\------

 

The Doctor came to once again, he could tell he was in a bed and not on the floor, hearing the gentle beep of monitors and a hand keeping hold of his. “Clara?”

“Hey sleepy head you finally woke up.”

He opened his eyes looking to her, her hair was visibly longer almost to her shoulders, the glow of pregnancy fully on her, “How long?”

“Four almost five months.”

He smiled softly as he was still waking up, “boy or girl?

She grinned, “Girls.”

Her looked at her in confusion, did she purposefully say what she said? “Girls?”

“Twins.”

“Bet everyone is treating you like a queen, twins are rare.”

Clara giggled, “You're right but I'm glad you're awake finally.”

“Oh why is that?”

“I wanted you to be there I was getting lonely.”

“I'm trusting that Jack was taking care of you, what happened?”

“Yeah even Amy is helping out but I wanted you, been sitting here a lot when I could. I wanted you to experience everything with me.”

He smiled, “Glad I woke up then.”

“Oh!” She quickly grabbed his hand placing it on her large rounded belly to which he felt movement of one or both of the babies shifting.

Startled the Doctor sat up a little too quickly as he made himself a bit dizzy but he pushed through it as he put his other hand onto her feeling the movements, his face in surprise. He looked up to her, “what did you want the other name to be?”

“You pick, I chose Idris.”

“Rose.”

 


	19. Chapter 19

Clara was grateful he had woken up, she didn't admit it those months back but she was scared and she wanted someone who was equally as scared as her to be with her. She moaned softly as the Doctor rubbed at her lower back, as she sat topless between his legs on the bed, the last month of pregnancy was a blessing and a curse as she was very uncomfortable but knew it would end in a few weeks.

He kissed at her shoulder tenderly, his hands now just softly caressing her back, “better?”

“Yes,” she leaned back against him, his hands rubbing at her shoulders, “did you ever think this would happen?”

The Doctor became quite still, he had faced some of her hormonal episodes at the wrong words but he didn't want to lie but knew telling her the truth might set her off till he thought back to what Idris has said. “Well saying we had a lot of sex it would eventually happen.”

Clara laughed and leaned her head back against his shoulder, “Well not with twins.”

“Twins are a surprise, yes.” He grinned lightly kissing the corner of her mouth then trailing along her jaw and neck soliciting a moan from her once again.

“I'm so tempted to say screw the 'no stressful activity' recommendation the doctor gave me,” Clara giggled, “gets me out of talking with those damn machines though.”

“You were the one that thought it should be you to take my place while I was in the coma,” he slightly smiled still teasing her with light kisses against her neck and shoulder.

“Yes because you would be upset if someone else would have,” she groaned in a slight frustration that was now growing, “John if you keep this up we're going to have to do something about it.”

The Doctor chuckled at her use of his real name, kissing and now adding a slight nibble to her shoulder, “Absolutely right about everything mum.” His hands moved forward cupping her swelling breasts his fingers dancing across her nipples making them harden.

Clara moaned loudly, a lot louder than she would have probably done before but her body was so sensitive it was done on instinct. She could swear she felt the smile on his lips as he grazed her neck but she could definitely feel the erection he was gaining as he pushed up against her. Her hand gripped at his hair as found the sensitive part of her neck suckling gently at it while his fingers rolled the hardened nubs of her nipples bringing her to a very surprising orgasm.

“You alright?”

Clara let out a breathless laugh, “yeah, that was sudden.”

He smiled his hands rubbing on her arms, “another or don't want to push it?”

Clara groaned a bit, she very much continued on to be damned with doctors recommendations but it was their first, twins at that, so she didn't want to take any chances, “As much as I hate following directions, doesn't mean you should be left out though.”

“There will always be other times.”

She shifted in the bed getting onto all fours making the Doctor lay in bed with her cuddling, the best she could, up next to him, “Doesn't mean you should wait.” Her hand unzipped his pants pushing them down before gently grasping his throbbing erection stroking him slowly.

He pulled his shirt off and worked the best he could to shove his pants down more for more freedom as she continued her strokes moving down to bring her lips onto the tip, softly kissing before bringing her tongue out slowly lapping up the precum. He groaned as her tongue teased him before she engulfed him fully into her mouth, sending him over the edge within a few quick moments spilling into her mouth.

The Doctor groaned as he laid in bed catching his breath with Clara rejoining his side, “looks like I was just as excited.”

She giggled, “nothing wrong with that.”

He smiled pulling his pants back up and rubbed at her arm, “true it's not like we're trying for kids either.”

Clara smiled and winced, “Ugh I don't understand how my back is hurting again.”

He frowned watching her movements to see if something else was going on than back pain, “did you want to go to medical? You've been hurting somewhat regularly the past few days.”

She shook her head, “I don't think anythings going on apart from annoying back pain from carrying two very active babies around.”

He chuckled kissing the top of her head, “alright but don't be afraid to say you need to go better safe than sorry.”

“I'll be fine I have you.”

 

\------

 

The Doctor gently woke up from his sleep, the few hours he always got during the night, and slid out of bed not wanting to wake Clara from the desperate sleep she would need. He heard a soft tapping at the door, luckily he was awake as it was just barely audiable. He opened the door and looked around till he looked down seeing a young boy looking up to him. “Yes?”

He stuttered, obviously scared at the grey haired adult that was accidentally looking at him angrily, “The council requests the ambassadors presence.”

“The ambassador is asleep and on bed rest, also known as no.”

“It's important. They told me to try everything I could to get the both of you sir.” The boy looked nervous, “Idris asked for you.”

He looked at him oddly, “How do you know that name?”

“The weird woman told me.”

“Stay here.” The Doctor rushed back inside grabbing a shirt and kneeling down at the side of the bed softly rubbing at Clara's arm, “Clara.”

Clara groaned, “I just got to bed.”

He spoke softly at her trying to wake up, “Clara you need to get up the council is asking for us.”

“They can fuck off.”

He laughed, “quite right but it's something about Idris.”

“She's gone John let it go.”

“I did but the messenger just gave me her name.”

“You can go I'm sure they'll understand.”

“Okay, don't get scared by the messenger boy I'm going to keep watch over you.”

“Whatever.” She rolled over to her other side determined to stay asleep this time around.

  
He walked back out, looking down at the messenger boy, pointing into their quarters, “You stay here and keep watch of Clara run to me if she needs me alright? Don't eat everything either, otherwise the pregnant woman will devour you.”

The boy eyes went wide and nodded slowly, “Y-yes sir.”

 

He ran as fast as he could across the colony making his way to the council chamber being greeted by the chairwoman, “Why is Clara not here?”

He caught is breath for a moment before standing up straight looking towards her, “Sorry we had a late night, back pain. I tried to get her to come along but I have to remind the council she is on bed rest and we're actually following it.” He looked around the room, “the boy said Idris.”

A very, very familiar voice, one that did not come from a speaker, came around from behind him, “Yes my thief, he did.”

 

**Notes for the Chapter:**

> Well I thought this was going to be the last chapter BUT story changed up a bit. Enjoy :)


	20. Chapter 20

The Doctor stared at a neatly dressed version of Idris, her hair no longer the craziness that it had been but smoothed and put into a bun. _No this is impossible_ , he thought his mouth slightly open trying to find the words.

Idris held out her hand towards him in offering to touch her, “I am real as real as a machine could get.”

He took both of his hands and took hold of her offered hand feeling at the skin and bones, the skin by far felt very real but the muscle and joints underneath felt unusual. “How is this possible? Though the question is why?”

Idris nodded calmly, “The skin was grown and molded to replicate my avatar inside the matrix, robotic body of course.” Her other hand reached up to take one of his that was feeling up her arm at the oddness of the machinery inside, “We thought it would be more appealing to be more human to put everyone to ease.”

He turned to the chair woman, “Who else knows about this? We both know everyone would go into a craze knowing she was here and like this.”

Idris frowned, “Then why did you share me with the council all those months ago?”

The Doctor sighed looking back to her, “Well that's how you used to look. Everyone knew you were a machine. This,” he gently pulled he hands away pointing at her form, “is very, very different and can – will be frightening to a lot of people, treaty or not.”

The chair woman spoke up, “That is why I am entrusting you to take care of her. Only you, Clara and myself know of this, the crew that picked her up have no clue.”

He took a few steps back so he could put his view on both women, “So what's going to happen when the mob finds out?”

Idris cocked her head, “I do not understand why you are now against this my thief.”

“I'm,” he sighed, “I'm not. God how I'm not, I'm just thinking of the bigger picture for a moment.”

The chair woman nodded, “Yes I fully well know of what could happen as well but there is a peace treaty between us now. Idris is the ambassador.”

The Doctor looked in surprise, “Please say Clara won't have to go to the machine city?”

She shook her head in reply, “That will still be dealt with through the matrix or through Idris.”

Idris softly smiled as the Doctor looked back to her, “How is Clara and the child?”

“Twins, she's having – will be having.” His mind was still thinking about what would happen if people found out about Idris and looked back towards the chair woman, “I understand the whole point of her staying with me but Clara - couldn't she stay with Jack?”

“I asked specifically for you Doctor.”

He mumbled repeating what she had said while rubbing his face in an almost slight disbelief, he was ecstatic that she wasn't dead but he wasn't thrilled to have her here in the form that she was. He huffed and took her hand, “Alright, alright, alright. I need to go back to Clara anyway she's been uncomfortable these past few days.”

 

Idris and the Doctor walked back to his quarters making some small talk about what had happened when they parted. Idris was indeed decompiled but not destroyed as it had been deemed necessary for someone to help the machines with coming of terms with their new emotions. They received a few glances as they past by people but were brushed off to the Doctors surprise.

“Well here we are,” he opened the door to the living area seeing Clara sitting up reading to the messenger boy that he had told to stick around.

“John hey,” she smiled the tiredness was still visible in her eyes, “David here didn't know how to read so I was starting to teach him.”

He smirked letting go of Idris as he walked in and sat down beside the two, “well a good reward for watching Clara. Thank you, you can go run off now.”

The young boy nodded, then looked nervous before he spoke again, “c-can I come back? I was enjoying the book.”

Clara smiled, “I don't see why not though there might be a time where I won't be able to.”

Idris spoke up walking into the room fully, “I could teach the boy once you are occupied.”

Clara looked up in surprise, “Idris?”

Idris smiled, the first time she truly smiled before either one of them, “Yes, hello.”

“I thought I was dreaming when John said you were here,” she laughed a little, “I would get up but these two are making it difficult to do anything.”

“It is alright.”

David scooted out of his spot and hugged Clara, who hugged in return, “Thank you. I'll be back!”

Clara grinned as he ran off out of the room and then looked to the Doctor. “Can we keep him?”

He laughed, “He's not a pet Clara and I'm sure he already has a mother. Plus we're going to have two of our own very soon.”

She smirked and rubbed at her stomach as the daily kicking fest had started, “Real soon I hope, getting real crowded.”

“May I feel?”

Clara nodded and watched Idris place a hand on her stomach trying to feel the kicking, “Here it's over here.” She gently pulled her hand over to the right spot, “I take it you're the machine ambassador?”

Idris nodded, “I am to live with you, treated as a matrix born that is aligned with the machines. No one will know until both parties feel it is time to reveal the truth.” She moved her hand to a different spot in surprise to Clara, “My thief mentioned you were in discomfort.”

“Why is something wrong?”

“Your body has been preparing for labor, it is only a matter of time as I can feel the slight movements. You are having pain now?”

Clara nodded, surprised she had guessed right, “Y-yeah just some stubborn back pain it goes away after a while.”

Idris smiled, “What are to be their names?”

The Doctor spoke up finally after watching the interaction, “Rose and Idris though with you now here we need a new name.”

Clara frowned, “Why not keep it? I doubt Idris would mind.”

Idris smiled, “I would enjoy that. Though it would be very confusing if the child and myself were in the same room together.”

Clara giggled, “We'll think of something.”

 

**Notes for the Chapter:**

> Apologies that my chapters are spread out once again. The overwatch beast has taken me hostage again. 
> 
> Thank you all for reading and hope you're enjoying this.


	21. Chapter 21

Clara woke up to having to pee for the nth time that night and came back realizing the bed was empty, it wasn't rare to wake up without the Doctor but as she looked around she realized he was gone. She waddled back to the front area where Idris had been sitting reading a random book she found before looking up to Clara. “Idris where did he go?”

Idris had a small amount of concern on her face, “He said he was needing to walk around, could not sleep. Are you alright?”

Clara nodded and worked herself into a seat, “yeah, first time he's gone out without letting me know.”

“He is very worried.”

Clara chuckled, “Not the best time to walk around if he's worried about me.”

Idris smiled, “Agreed though I believe it is not just you he is worried about. He is worried about you, raising two children and how this colony will react when they find out I am a machine.”

“Plus the fact that he is bored out of his mind.” Clara chuckled slightly, “he wants to go back into the matrix. I don't understand why.”

“He enjoys running, the feel of the adrenaline of almost getting caught unfortunately but he will be disappointed as that is no longer the case due to the treaty.”

Clara smirked and then sighed as she thought, “Do you think he'll try to keep running?”

Idris tilted her head in confusion, “I do not understand what you are asking.”

“With what you just said, he can't be the Doctor anymore because he can't cause the mischief he used to do, he's just John. Is he scared of the real life?” She shifted as a twin shifted causing to wince, “is he scared of this?”

“Are you not scared as well?”

Clara giggled, “Horrified but I think I'll be a good mum. Been practicing with David.”

“You have been reading to David to teach him. I do not see how that is practice.”

Clara smiled, “He's an orphan he told me himself the other day. He wanted me to be his mother.”

“Does he not know you are pregnant with children of your own? You can not take care of --”

“Idris,” Clara gently grasped Idris' arm making her stop, “he knows, he's excited to see them. You should have seen his little face when I said I was having twins. He was so enthralled that a mum could have more than one at a time.” She leaned back smiling rubbing at her stomach once more, “I told him I would gladly take him in. I was hoping to talk to John this morning about it.”

Just as Clara finished her sentence the Doctor walked in carrying a small bag filled with unknown items with David rushing in in front of him running up to Clara, “Whoa there, he's a little excited for today's reading I see.”

Clara giggled as she got a big hug from the small boy, “actually there's another reason why he's so excited. I was hoping to talk to about this but I see someone couldn't wait.”

David turned around and grinned, “miss clara said she would be my mommy.”

The Doctor looked at Clara in surprise, “Clara why would you do this?”

“Please don't argue he's all by himself John he needs someone to take care of him.”

“The council was already taking care of him; he eats, has clothes --”

“Runs him around like a puppet, doesn't bother with teaching how to read or how the world works or how it should be. He would just go into the militia and be a solider taught to kill machines.”

He raised his eyebrows in surprise and looked to Idris who was calmly watch the two of them, “is it alright for him to stay?”

Clara looked at him confused, “Why are you asking her?”

Idris smiled, “it goes back to him being worried about the colony finding me out.” She looked over to David, “you questioned me why I was so awkward – weird as you put it.” David nodded in response which Idris leaned over, “before I give you the correct answer I want you to know I've known the Doctor for a long time, Clara knows me as well, so I do not want you to be frightened by what I am going to say; I am a machine.”

The Doctors jaw dropped looking at Idris in horror, “Why did you just tell him?! He's going to go around and tell everyone!”

David was totally ignoring his outburst as his eyes lit up, “Really?! You don't look like a squid though. Can you show me?”

Idris smirked, “I can not truly show you as I would hurt myself but there is one difference between me and everyone that was connected to the matrix.”

“What's that?”

Idris turned shifting the hair out of the way showing the port, like all matrix born had, at the back of her skull, “this is the only connection I have. Everyone else has the small ports around their arms and body but I do not.” She turned back around pulling up her sleeve which would have revealed a few ports by now. “Also as the Doctor has put it my body is more rigid to that of a human.”

“Do you hug?”

Idris smiled putting the book she had been reading aside and stretched her arms out which David walked over and gave her a hug, “is this acceptable?”

He nodded and giggled, “you do feel different.”

They broke the hug with Idris still smiling, “know this, I will never harm you or anyone in New Zion.”

The Doctor knelt down quickly to David taking him by the shoulders, “don't tell ANYONE. Do you understand?”

Clara frowned, she would have stood up to rescue David but her condition wasn't going to let her, “John!”

“Clara please I don't want anyone to get hurt if they found out.” He squeezed at the boys shoulders, “please.” David nodded, a little scared at the action, to which the Doctor smiled, “good, good. I'm sorry. Sometimes adults can over react to things and this is one I don't want to let happen.”

David moved over to Clara whom put her arms around gently and whispered in his ear, “it's okay there's a bed in the other room for you to take since Idris doesn't sleep.” She waited till he rushed off with his bag and looked to the Doctor, “and YOU will promise me you won't ever do that to him or to our daughters ever again!”

“Clara,” the Doctor sighed, “I'm sorry. Please really please understand I don't want to wake up in the middle of the night having all of us hauled off by an angry mob.”

Idris frowned, “I will be the only one being taken and possibly members of the council.”

Clara huffed and shook her head, “John we're going to the chair woman and ending this stupidity now.”

He looked at her, “What?”

“We're going to gather everyone up and tell them that Idris is a machine. Let them decide.”

“After the babies are born.”

She narrowed her eyes and slowly stood up, “No, now. David come on we're going out.”

“No it's not a good idea for you to be walking what about the babies?”

“John,” she sternly said his name by this time, “they're fine, it's just early labor the doctor was worried about and quite frankly we've passed that worry point so as of right now I would rather have them come out while we fix this worry you have.”

He sighed, “Clara --”

“Now!” She shouted and walked out with David and Idris in tow.

 


	22. Chapter 22

“I apologize for such short notice of this meeting we will be informing the others in the field shortly there after so they will know the situation,” the chair woman spoke towards the gathered crowd with the other council members with Clara and Idris nearby as well. “While I would have liked to have waited for this, our ambassadors have highly requested that we do this now, and I will let them take over.”

Clara and Idris walked up taking the chair womans place with Clara starting, “I know some of you have some questions on who this woman is and why the chair woman had said ambassadors.” She paused looking at the crowd before continuing all, “This is the machine ambassador Idris and when I do say machine ambassador, she is in fact a machine.”

The gasps, whispers and a few shout outs of surprise made its way around till it quieted with Idris stepping forward a few steps. She nodded with a stoic face before speaking calmly, “What I am going to say some of you will question, it is only human nature especially for what has happened between Zion, New Zion and Zero One.”

Idris looked over to the Doctor and David who decided to sit with the masses, only due to the fact they were forced to, before looking to the crowd once more, “This announcement was meant to be told in a few months as you all got to know me but the Doctor had fears that once you found out on your own a riot would be incited. I was made to look human as it would be easier to fit in,” she looked to the Doctor once again, “in fact apart from my skeleton and brain I am as close to a human as a machine can get. ”

The Doctor stared at her in surprise till a voice yelled out from the back of the crowd, “See they're looking like us so it's easier to kill us! It's probably telling them where we're all at this moment!”

Idris stood there still with a stoic look on her face, “I can assure you I can not communicate wirelessly with Zero One, they do request that I make regular updates so they are knowledgeable of my well-being and of course of any changes that need to be addressed.”

Clara stepped up beside Idris as the mumbles and whispers were growing angry, “Please! She has been in our care for a week already just reading, talking with us and even teaching a young boy to read. She might be a machine but she hasn't hurt anyone.” She frowned towards Idris who looked saddened as well to the groups reaction.

“You should sit down you've been standing for too long,” Idris softly spoke to Clara noticing she was swaying trying to keep herself occupied on something else.

Clara shook her head, “I'm fine.”

“You look uncomfortable.”

Clara smirked, “Of course I am, you try being nine months pregnant with twins while trying to calm a city full of angry people.”

Idris smirked in reply, “Very unlikely as this situation will never happen again and twins are a very rare occurrence.”

Clara looked very confused at Idris, who had smiled for a quick moment before another member of the crowd shouted at them forcing her attention back to the matter. “Listen! Will armed guards with her be acceptable? Either way she is staying here it is apart of the treaty.”

The chair woman walked back up to the two addressing the crowd once again, “I will take responsibility for hiding this information from the council and all of you. I want everyone to give her a chance for one month, without the armed guard, and at the end of that time period the council will decide my fate and Idris' as well. You are all dismissed and free to go about your lives but take note, she is to be considered a citizen. Any harm to her will have consequences.”

 

\------

 

“Clara is everything alright? You're squeezing my hand pretty hard.” The Doctor looked to her in concern as they were walking back to their quarters after the gathering of people had dissipated.

“I think I should have listened to Idris about sitting down,” she paused leaning against the railing wincing in now a very apparent pain, “can we go to the medical wing? I think we're close yeah?”

“Can you even walk there?”

She nodded, reaching for Idris who came up onto her other side helping her to walk, “Idris could you take David home?”

The Doctor looked at her in surprise, “Clara I don't think that's such a great idea. I don't want Idris alone.”

“John please don't argue, really not the time.” She gasped as the pain had changed to something different and stronger, “yup, really really not the time. David probably knows shortcuts to get home quicker, shut the door let David answer.”

Idris smirked out of amusement and nodded still holding onto Clara, “Let me assist with walking you to the medical area first you might need it.”

 

\------

 

David looked up to Idris as they sat on the sofa in the living quarters after helping Clara and the Doctor to the medical area,“Is mommy going to be alright?”

She looked up from her book towards the young boy that had a serious state of worry on his face, “Yes of course she will be alright. Why do you ask?”

“She was crying.”

Idris nodded, she thought how to put it in simple terms for him to understand, “When a mother goes to have a baby, in Clara's case two, her body is pushing the baby out and it causes a lot of pain for her. Do you understand?”

He nodded, “can you have a baby?”

“Why do you ask?”

“Can you?”

She smiled, “Well if you promise to keep it a secret I will tell you.” She watched him nod and smile to her, “I can, Zero One wanted me to experience everything a human does so we could understand humans better.”

“But I thought you already knew everything about humans?”

“Oh yes we do but in a biological way, how your body works, not why you would want multiple children in a place that really has no jobs, where you have to fight for your lives.”

“There are jobs I wanna be an operator!”

“An operator? Why would you want that?”

“Well I can't go into the matrix like you so that's as close as I can get to see it.”

Idris smiled, “That is why you are wanting to read?”

David nodded, “Also to make the other kids stop making fun of me.”

“I can guess that some of them can not read either.”

“You think so?” he questioned as he started to yawn.

“It is a good guess that at least one of them can not.” She smiled softly, “judging from your yawn it is getting late, you should go to bed.”

David frowned giving her tired puppy dog eyes, “I wanna wait for mommy.”

“It could quite possibly be a long time before you can see her. It would wise to go to bed, sleep will make the time pass. I can read to you.”

David smiled getting up and rushing to his bed with Idris following sitting in the bed with him as she read him to sleep.

 


	23. Chapter 23

Idris slowly opened her eyes to the Doctor sitting on the edge of the bed smirking at her still sitting up with David having slumped over falling asleep in her lap. “I thought you didn't sleep?”

“I wanted to see what it was like.” She smiled noticing a bruise on the Doctors cheek, “how did you injure yourself?”

Embarrassment rolled over his face as he blushed bright red, “evidently I'm squeamish of blood in real life, passed right out when the first baby was born.”

Idris started to giggle, to the surprise of the Doctor, but it quickly died off as David started to shift almost getting woken up by the commotion. “We should take the discussion to the other area.” She tried to shift from under David but it was proving difficult, “I could use assistance with David.”

He smiled as he got up and moved to the other side gently and as carefully as he could lift the young boy up freeing Idris of his weight. “I would have figured you could have easily got from underneath him.”

“Yes but it would have woken him up and he has been worried about Clara since we left.” They stepped out of the room and sat at the table far enough away so they could not wake up David, “How are Clara and the children?”

The Doctor grinned, being the now proud father that he was, “Resting ,they're so beautiful you should see them.”

Idris smiled to him, “You should sleep as well it has been a long day.”

“Slept when I knocked myself out. In fact I have questions for you.”

She nodded knowing what he would be possibly going to ask, “this is about my comment about being human.”

“How human are you?”

“Fully functioning, in every way; sleep, eating, sexual -”

He held his hand up to stop her from going any farther, “What was their plan because this isn't a coincidence.”

“I was put here to be a gateway for New Zion to discuss initiatives that needed to be done, ways that both cities could help one another out and to learn more about humans by putting a fully biologically functioning cyborg into the city that already had a grasp on how humans acted. I am here to eat, sleep, breathe, walk, philosophize and thousand more ways with you, with humans.”

“What is their plan Idris?”

“No plan why do you not believe me?” She sat up looking at him in a more serious light, “it's because I'm here isn't it? I'm not gone like you believed I was.”

“I am not going to lie to you but yes.” He looked down at his now fidgeting hands, “I made my peace with you gone, almost died because the emergency jack out failed again.”

Idris gently placed her hand onto his, “I know I was hoping to talk to the doctors that treated you to see how I can fix it, I want that program to help everyone. I really do.”

He smirked chuckling a moment taking her hand into his looking at and feeling her skin before feeling the pulse at her wrist, “little fast for a heart beat.”

“It is just right for the conditions.”

“Oh?” He looked up to her blushing slightly and spoke again in realization that the heart beat wasn't wrong but right in response to his touch, “oh.”

“It was not going to be me that was to be the ambassador, in fact Zero One recompiled me so I could choose the program. I managed to to state that I would be the proper choice due to my relationship to you.” She looked down at his hands, “it was so I could go back to you. I do not want to go back.”

“Idris it sounds like you stole this body and ran away instead of being the ambassador.”

“I did, I stole this body. I don't want to go back, I don't want to converse with them anymore. I want to be here with you, Jack, everyone.”

He pulled his hands away from hers looking at her slightly concerned, “This is the first time I heard you say don't instead of do not.”

“I finally was able to comprehend contractions.” She started to giggle once again, “I remember when you tried so hard to teach me in the first year because you didn't want me to draw out my sentences any longer than they were.”

The Doctor smiled, his relief that she hadn't been replaced by something else, “so if I were to ask you how long we've known each other?”

Idris grinned, “Over ten years.”

“Why did you hide all this?”

“I didn't want to frighten you, any of you that I am finally human.” She smiled almost excited she could be 'normal' now, “this body has freed me of all those restrictions I had. I love to smile, laugh I know what feeling in love does to the body. You felt my heart racing because of it,” she paused making sure their eyes were locked at each other, “I want to kiss you.”

He chuckled nervously, “Idris this isn't the best time, well, will never be the right time.”

Her smiled died down as she became confused, “Explain.”

“I just can't kiss another woman while the one I am with just had my children.”

“It is just a kiss.”

He stood up, facing away from her, as he softly laughed about how the conversation was going, “will it be just that?”

“You are human.”

He shook his head determined to keep his answer, “Not a good excuse.”

“Then I will ask Jack.”

He spun around quickly. “No!” His shout surprised the both of them which he took a pause before continuing his sentence in a calm tone, “You will do no such a thing.”

“Why not?”

“Because your 'just a kiss' will be more than that with him.”

“If it leads to sex then that will be acceptable as well.”

“No.”

Idris smirked, “For someone making an excuse for not kissing me you seem very jealous over someone else kissing me instead.”

“Damn right I am.” He grabbed her hard, pulling her to him as they mashed their lips together for a few sparse moments before he pulled himself back from her.

Idris frowned, it felt forced as she knew he had feelings for her, but understood this was more of an attempt for her to not go anywhere else. “I understand. I am sorry I will not ask again.”

He sighed, “you know me too well.”

“As much as you do not understand me.” She smiled softly, “I am not here to replace Clara, I doubt I could, but I am making a simple request that will fulfill our curiosity.”

He nodded, “then we do this right. Ready?”

“Do you have to ask?”

The Doctor smiled loosening his grip on her arms as he stepped as close as he could to her as he looked upon her face before slowly leaning in, her arms gently grabbing his waist in turn, brushing his lips lightly against hers. A soft gasp escaped from Idris, as she had been accidentally holding her breath waiting, leaning forward opening her mouth slightly letting him in. They broke the kiss as the need for air was now a necessity and they looked towards each other smiling.

“Thank you Doctor.”

He chuckled a moment, “seven years wanting to do that, so thank you.”

 

 

**Notes for the Chapter:**

> Apologies for all the twists and turns hope they have been good.
> 
> And yes I (hopefully) made sure Idris never said anything in a contraction (don't, I'm, we're etc)


	24. Chapter 24

“I don't know Doctor,” Idris looked at the clothes that was handed to her, “would Clara be upset for me taking them?”

“I doubt it. She hardly worn that but I think it was due to carrying the twins.” The Doctor smiled looking to her dress which was showing the signs of wear to it, “besides you've worn that ever since you got here, you should have more than just that. We can look through the market on our way to see her.”

“The market is not on the way.”

The Doctor frowned, “Idris.”

“It is late in the day I would not want to make Clara wait for you any longer.” She turned after hearing David creaking the door open to peer into the room, “plus I know David has been very anxious to see her and the babies.”

“Trust me she might tell us to come back later, there was a line forming once the news hit that she had the twins. We'll have enough baby blankets for 10 kids.”

Idris smiled and spoke to David who was very eager to leave, “David go back out to the other room we will leave in five minutes, I promise.” After he left she looked to the Doctor, “I need assistance with my dress.”

He chuckled nervously as he stepped towards Idris, her back to him, carefully unzipping her dress naturally eyeing the nakedness of her back. “Good thing you won't have to deal with zippers anymore.” He stared one moment too long as he watched her pull the dress off revealing her naked form before he averted his gaze and gave a quick cough.

“Should I have warned you?” Idris smiled as she pulled the light blue dress over her head.

“Warned me about what?”

“My nakedness?”

“Would have been nice since it seems you do understand privacy.”

“I don't understand why,” she walked into his view, “as this dress only covers up what is considered sexual to some.”

The Doctor did start to regret letting her borrow the outfit as the halter neck dress did leave her shoulders, arms and back uncovered but he quickly grabbed the other half of the ensemble, a white thigh length sweater coat, handing it to her. “There's this too.”

She gently put on the sweater looking at herself and then looking towards him, “I don't understand this.”

“Regardless of how close we are to the core without killing ourselves it's still cold.”

“Then robes would have been more logical.”

The Doctor chuckled, “you know I hate robes and plus you look lovely.”

Idris smiled, “Take David to see Clara I'll go to the market.”

He frowned and shook his head, “I'm not letting you go off alone.”

“I can handle myself Doctor plus I want to show that I am not afraid and that no one should be afraid of me.”

He sighed, knowing that nothing would change her mind, “But when it's one against a large group, unless you can bend reality, it does not end well.”

Idris nodded before going to the door to open it, “I will be alright.”

 

\------

 

“Mommy!” David rushed into the room with Clara sitting up with one of the two twins in her arms smiling.

She hushed him softly, “quiet both of them are sleeping.” She looked up to the Doctor who was looking over the other sleeping girl and noticed Idris was not walking inside the room, “Where's Idris?”

“I, um, let her go on her own to the market. I suggested we do it on the way here so she wouldn't have to borrow your clothes since she just had that one dress.” He gently rubbed the babys cheek before standing up looking at Clara with a slight look of concern on his face.

Clara giggled slightly, “oh that look, you are still worried about her.”

“Of course I am, didn't get nightmares from a crazed mechanical rabbit jumping out of me and neither did anyone else. She is a machine, a machine that now looks and acts like a human.” He sighed and sat on the edge of the bed looking at the other baby in Claras arms with David climbing up on the other side to look as well.

“I know but wasn't this what you wanted?”

The Doctor rubbed at the back of his neck, “Honestly I just wanted both groups to leave each other alone and that the people in the matrix to know that they were in the matrix.”

“Which one is this?” David peered over trying to figure out which baby was which.

Clara smiled, “This is Rose.”

“What happens if both of them want you?”

Clara smiled looking up at the Doctor, “That's where the Doctor and Idris come in they can help me.”

“Can I help?”

“I'll let you help with somethings.”

David grinned, “Okay.”

The Doctor looked around for the massive pile of items that he was expecting to be somewhere in the room but was no where to be found, “So what happened to the giant mass of twin worshipers?”

Clara giggled, “The nurses made them all leave but there is a lot of wonderful things for the girls.”

“No doubt.”

 

 

 

The Doctor stood around holding Ellie, they decided to change her name from Idris after the thought of having to call her out might be confusing, when there a gentle knock at the door with Rory poking his head in. He grinned walking to the door, “Rory, this is an interesting surprise. I take it you and Amy are here to see the girls?”

Rory politely waved to Clara before frowning a bit to the Doctor, “Actually no, um, I need to talk to you in private.”

“I'm sure you can say it in front of Clara if it has to do with her.”

He shook his head, “Idris was brought into the emergency wing along with the men that assaulted her.”

“What?!” He rushed over and handed Ellie off to Clara.

Clara sat up taking the baby into her arms looking to the Doctor, “John what's wrong?”

“What I hope wouldn't happen I'll be back, stay with Clara David.”

 

 

They both walked with haste with Rory filling the Doctor in on what happened, “She probably would have been in worse condition if she didn't have that metal skeleton of hers.”

The Doctor frowned as they turned into the area with him seeing a bruised and bandaged Idris in a bed, “Oh Idris, no no no.”

“Had to jack her into a construct to put her to sleep since her brain isn't biological drugs weren't working to help ease the pain.”

“How did you know to do that?”

Rory sighed, “She told us, especially after we tried injecting her with the meds. ”

His face saddened, almost on the verge of tears, “I shouldn't had let her go by herself.”

“You didn't know this would have happened.”

He shouted starting at Rory in anger, startling him and everyone around them,“NO! I knew it would happen yet I let her go!” He clenched his teeth as he walked off.

“Where are you going?”

“To the meet the assholes that did this to her.”

 


	25. Chapter 25

The Doctor saw no guards but saw four men restrained to beds, one which was the ex-council member looking not as worse for wear as his friends, “Of course it would fucking be you, what do you think she was going to do?”

The man glared the best he could with the swollen black eye he had, “destroy New Zion of course.”

The Doctor shook his head, “With what?!”

“It must have something in it. A nuclear device they've done it before.”

“Yet you kidnap her and beat her, smart if she did have a device it would have been set off. All she wants to do is live here with us.”

“No machine wants to live here.”

He shrugged, “Then I guess that means she's human.”

“It's a machine.”

The Doctor grew frustrated by the circular logic the man before him, “Do you think those screams of pain were for show? She felt the pain of you and your lackeys beating the shit out of her, she can't even be given drugs to fend off the pain, she's in agony right now because of it because of what you did.”

The man smiled laying his head back looking up to the ceiling and the glaring lights not caring it was blinding him, “Good getting what it deserves.”

The Doctor shouted loud enough that anyone could hear outside the walls, it was the straw that broke the camels back, “She did not deserve this! Nor any machine in Zero One deserved what we have done!”

The man looked back to the Doctor now getting just at frustrated at the dueling logic of each side, “They did this to us!”

“We did it to ourselves and you're going to start another war for the same reason. You're scared. Well let me tell you you shouldn't be scared of them but of me.” The Doctor went over to the mobile cabinets and started to search in each drawer.

“What are you doing?”

“What should have been done in the first place.” He lifted up a scalpel looking at it and then looking to him.

“You can't kill me.”

“Oh I'm not, I'm giving you a choice,” he placed the scalpel right on the mans chest, “you can leave and I don't mean from the ward but from the colonies or you can let the council decide your fate. I would let the council decide because it's cold out there and once the machines find out what you did, they won't be gentle.” The Doctor turned to the other three men who were watching the conversation with horror on their faces, “I think I can help at least get you and your buddy only life in a small cell but don't count on it.”

 

\------

 

The Doctor frowned at Idris' avatar in the construct, she looked like bad tv reception with the dull and fuzziness it produced, maybe her brain had been damaged or maybe the pain her body was signaling was really too much for her. He was just glad they let him speak to her, at least to let her know she was alright and she would get better.

She was sitting on the bright white surface her head buried into her knees as she was curled up, her voice crackled, “My thief.”

“Idris.”

Her voice crackled in pain, “Why did they do this to me?”

He knelt down beside her, eventually sitting down keeping in close contact, “It was Castellian. He's the one to blame, managed to round up a few scared people to do this to you.”

There was a long pause before Idris finally looked up visibly crying, “No one came to help me till I flung one of the men out of the alley way.”

He put his arm around her and his other hand thumbing away the tears, “Oh Idris I should have been there so they wouldn't have done this to you.”

“What's going to happen?”

“What do you mean?”

“They're going to make me go away.”

He shook his head, “No no of course not. I won't let them. I won't let them make you go back.”

“It hurts.”

He pulled her towards him more, “It's okay. You are going to have to ask Zero One to fix this, this isn't a way to live if you can feel pain without any relief.”

“I didn't know, didn't know how much it would hurt.”

“I-I know.”

A voice suddenly came out around them from out of the blue, “I'm sorry Doctor it's time to go.”

The Doctor sighed and softly kissed her forehead, “I won't leave your side.”

She buried her head into his chest just before he disappeared from the construct, “Thank you.”

 

The Doctor opened his eyes staring at the ceiling before Claras face came into view, “I shouldn't had let her go by herself.”

“I think I'm partly to blame with this, I wanted you to give her the freedom that she deserved and stop worrying over this.”

He sat up shaking his head, “No never going to blame you for anything it was all on me, she asked for me, I was to watch her and protect her.”

“John please don't do this to yourself. What's done is done.”

“She shouldn't be suffering.”

Clara caressed his cheek, “I know but beating yourself up for it won't help her get any better. She isn't going to blame you. I never blamed you for what you did to Danny.”

He sighed and turned his head away, “I'm a bad man.”

She smirked turning his head back to face her, “you're a very good, loving man. If you were a bad man would you think you would have so many friends?”

He scoffed, “Many friends, I don't see how you or Jack is many.”

“Vastra, Jenny, and all those other people who believe in what you do. They wouldn't blindly follow someone like that asshole Castellian they would follow you through hell before they would him.” She leaned over and kissed his forehead before walking off.

 


	26. Chapter 26

“Doctor you do not have to take me by yourself.” Idris frowned sitting in the co-pilots seat of the Tardis as the Doctor flew it to its location. She had surprised everyone with her injuries healing faster than normal till she had mentioned that the machines had perfect nano technology which aided in her healing, it was added just in case accidents did occur but was thought the healing would be fast enough that the need for accepting chemical changes (pain medication) would not be needed.

“Clara needed an extra hand with the children.” He sighed as he thought about Clara he had hardly seen her or the babies since the accident, which he was regretting just as much as letting Idris go by herself.

“Then it should be you instead of Jack. She told me you were a miserable wreck over me, just like you did over her.”

He continued to look forward as he traversed the ship through the tunnels at a faster pace than normal clearly wanting to get to their destination as soon as possible, “Idris, I don't want to talk about it.”

“Where are you taking me?”

“To the broadcast point.”

“So what was the reason for telling Clara you would be back in a few days?”

“You shouldn't be eavesdropping.”

“Difficult when my hearing is better than a humans.”

It was a few minutes of silence after her remark before the Doctor slowed the ship and parked it in a clear out space of the tunnel before getting out of the seat heading towards the jump seat area, “We're here.”

 

 

Idris sat back up after the meeting with Zero One looking to the Doctor who sipped at a cup before handing it to her, “drink.”

She took the cup and looked at the clear liquid, “I am not in need of any fluids.”

“Well not in need of the right type of fluid the body needs but we need to test that the change works.”

She sniffed at the cup smelling that it wasn't odorless but definitely of a strong type of alcohol. “I do not see how this would test it as it – I feel foolish.” She chuckled as she came to the realization of what alcohol does, “you told me to state that I need to accept any chemical that can effect the brain.”

He nodded, “drink up I'm already a cup ahead and I don't know how well your body deals with liquor.”

“I do not know why you want to use alcohol when you could use medication.”

“Wow you're being thick. Proper meds aren't easy to come by Idris, I'm not going to waste precious resources when there's a few liters of very easy to make moonshine in the cupboard to test out your body.”

“I don't understand why you need to drink as well.”

He smiled as he was already starting to feel the effects, “No one should drink alone.”

“So you did know that it would not take me long to have the update.”

He nodded, “I said a few days just in case the hangover was rough.”

She held up the cup, “you also said you were ahead by a cup this is only half you should fill it.”

“Cup and a half then.” He grinning grabbing the nearby metal jug and poured in more almost overfilling it, “though I would take it slow who knows if --” he stopped as she started to hastily drink the cup down to the last drop before coughing, “Okay.”

She smirked and held the cup up once more, “One more then I'll slow down.”

 

\------

 

The Doctor groaned as he opened he tried to open his eyes but the lights above blinded him making him groan once more turning his head away and shield his face with his hand for a moment before bringing it down upon something unfamiliar. It was smooth naked skin not of his own, he slid his hand slowly feeling that it was of a back, the lungs breathing relaxed and calmly, a spine without connection ports, feeling up to hair around the shoulders and underneath feeling the port at the base of the skull. It was Idris, a very naked Idris in fact as he didn't feel clothing on then again as the rest of his neurons started to wake up he realized he was just as naked as well as they laid together in the reclined jump seat.

His mind raced, he had slept with her albeit under the influence of Jacks moonshine, Clara would understand nothing would come out of it. _What happened on the Tardis would stay on the Tardis_ , his mind repeated the line adding in that Idris would keep it a secret, nothing would get her to break her silence as well. He caught himself still softly trailing his hand over her skin, it was warm and soft practically flawless.

Idris softly made noise, he didn't know if it was a groan of pain or one of waking of, she slowly shifted sitting up straddling his lap once more so she wouldn't hurt him, speaking in now a very groaned tone, “is this what a hang over is?”

He smiled as he slowly opening his eyes trying again against the blinding light and looked up to her, her head fortunately blocking the light shadowing her front slightly, “tell me how you feel?”

“Tired still, body aching, head hurts, I do not understand why my head hurts when the brain can not feel any pain.” She groaned once again leaning back to stretch.

His eyes wandered down her body, her small mounds of breast gently heaving with her breath, down across her stomach just as smooth as her back till his eyes stopped to her hairless pussy sitting on top of his hips. He cleared his throat to stop himself from looking much longer as the tingle of arousal was starting to form between his legs, a memory that all but his arousal had forgotten.

Idris giggled softly, having caught him looking at her, “you do not remember last night do you?”

He shook his head, “do you?”

“I can only recall up to the point of you having me bent over taking me from behind after stripping me of my clothing and bringing me to orgasm with your hand as you sucked on my nec-- ”

“Idris!” He shouted to stop her from saying anymore of her memory, it was too late though as his body was starting to betray him, “I-I really need to teach you about just saying 'yes somewhat' the next time someone asks you if you remember.” He inhaled deeply trying to clear his mind and calm his growing erection, “we should get going.”

“What is the rush? We have another day left,” she leaned back down against the Doctor, his hands instinctively taking hold of her hips gently, “I would like to experience last night once more with out the intoxication.”

“I-idris we shouldn't.” He moaned as she gently slid her core over his almost complete erection, “I have Clara.”

“You also have me, you are not bound to her, you are free to mate with anyone you please.”

He groaned, he hated machine logic and hated that she still thought that humans were animals, “Idris I am she had my children. I am to help her take care of them.”

“Yet you took me to the broadcast point,” a soft moan escaped her lips as she grinded her hips against him, “became intoxicated and had intercourse with me. You also kissed me out of jealousy of the thought of me being with Jack.” Idris grinned her face getting closer to his, his erection in her hand as she rubbed the tip against her hot entrance, “maybe I should ask Jack.”

The Doctor grunted as his hips lifted sliding himself into her tight wet tunnel, moaning as Idris gasped in surprise by him filling her so quickly. “The only thing you're going to ask him,” he thrusted into her once more, “is how he feels knowing he wasn't the first to touch you.” His hand went to the back of her head as they mashed lips together, sucking at their lips and rubbing their tongues together, as he thrusted roughly into her.

Idris guided his arms one by one to their respective arm rests before locking them in place to the Doctors surprise. She sat up slowly rolling her hips against him before leaning down against him again, “too quick, I want this to last.”

He groaned, “you were watching us weren't you?”

“Yes by your body language you enjoyed this very much,” she kissed along his jaw and down his neck.

“Oh fuck,” he groaned once again as he thrust his hips up in response feeling her wet cunt pulsate and hearing her moan out her orgasm into his ear. “I don't think I can hold out for another,” he now panted.

Idris sat up leaning back as she slid against his cock, squeezing around him purposefully, “cum for me.” It was the magic words that caused him to groan burying himself deeper as he spilled inside of her. Idris leaned back down releasing the restraints as she gently planted a few soft kisses on his lips, “thank you.”

The Doctor caught his breath, kissing her back, “Don't tell anyone about this.”

“What about asking Jack the question about --”

“It was sarcasm Idris. Very aroused sarcasm.” He sighed as he felt the regret settling in, “never tell anyone about what happened. Ever.”

 


	27. Chapter 27

With Idris now apart of the population she chose to live in her own quarters, which were a few levels below their living space, which let Clara and the Doctor have some alone time to themselves by letting her have David and another trusted body have the twins when they needed a break. Idris had also become Davids tutor which made him ecstatic come every Wednesday as they would read through a favorite book though on this particular Wednesday Clara was surprised to see David come back after an hour frowning and head hanging down. “You're back home early, everything alright? I know Idris always keeps Wednesdays open for you.”

“Idris said she wasn't feeling well,” he sighed sitting down at the table, “I didn't think machines got sick?”

Clara walked over the boy sitting down next to him, “you forget though she isn't really a machine, remember how she got hurt?” She waited till he nodded playing with the book they had been reading for his tutoring, “well she can probably get sick just like us.”

The Doctor walked in from the other room a crying four month old in arms, “Clara I think Ellie needs a feed.” He looked up seeing David at the table sulking, “Oh what's going on?”

“David said Idris wasn't feeling well.” She stood up gently taking Ellie from him to which the babe calmed down, “and evidently someone just wanted mummy huh?”

He chuckled, “guess so.” He looked to David, “I could teach you today if you want David? And I'll go check on Idris.”

David shook his head, “nah it's alright. I can wait till next week.”

“Hey, hey,” he knelt down beside him, “Idris loves reading to you she told me herself. She gets as excited as you do.”

“What if she stays sick?”

The Doctor frowned, as they had found out Davids mother had been sick which is why he had been an orphan, “Nope she has those awesome little robots inside her to help her remember? I'm sure she'll be right as rain next week.” He stood back up, “I'll go check on her now if that will make you feel better?” He nodded with the Doctor smiling in response looking to Clara, “I won't be gone long, will you be alright?”

Clara smirked, “Yes I have David here.”

 

 

 

The Doctor knocked on the door hatch to Idris' quarters, waiting a longer than normal time before she opened the door to which was just a crack so she could see who it was. “Idris what's wrong?”

“Inside now.” She opened the door wider pulling the Doctor inside to his surprise.

The Doctor regained his footing and turned looking to Idris checking her for anything wrong, “Idris are you alright? Did someone do something to you?” He started to look concerned looking at her.

She turned around looking at him, “I am fine.”

He continued to eye her up and down, there was no noticeable bruising, cuts or scraps but the grey flowing robes hid almost every inch of her skin from the neck down,“Why did you tell David you were feeling sick?”

“Because I had been.”

“Well then I can get David so you can tutor him today.”

“Not today.”

He raised an eyebrow still confused on why Idris did not want to see David today, “Why not?”

“Not feeling well.”

“But you just said you're fine.” The Doctor frowned, “tell me.”

Idris looked at the Doctor with a look on her face as she was going to regret the words she was about to say, “I am pregnant.”

“What?”

“I am three months, one week and two days pregnant.”

“Y-you want to say that again?”

Idris' face saddened grabbing his hand and placing it against her lower stomach, which was protruded slightly hidden behind the flowing dress she was wearing, “I am with your child Doctor. I did state I was a fully functioning human but you ceased my explanation of all my functions.”

“O-oh, oh god.” He looked around trying to find a seat as his knees started to buckle only to find the sofa that had been right behind him before he fell to the floor sitting in front of it, “w-why didn't you tell me?!” His body shook as his mind raced with hundreds of questions.

“I did just tell you.”

“No I meant why didn't you tell me on the ship?” He looked up to her with now an angry glare, “why didn't you stop yourself?”

Idris looked to him in surprise and then looked down her hands gently rubbing at her stomach, “I-I will terminate the child if this is what you want.”

The Doctor rubbed his face as he sighed, “no, no, no.” He sighed once more speaking in a calmer voice, “I just want to know why you didn't tell me.”

“I wanted your child.”

“Well you have it but that's not a good reason.”

Idris sighed and sat down on the sofa next to him, still on the floor, “I lied about Zero One's plan, only in the case that it was not malicious in its intent.”

“A hybrid child?”

She nodded slowly, “it was to be parented by a machine and a human of superior strength and intellect to be the true ambassador between our societies.”

The Doctor started to laugh, “w-why would you think someone would be alright with parenting a –,” he paused and looked at her, “oh you're sneaky Idris. You knew I had feelings for you and would be more than willing to do this.” He continued to look at her as he stood up, “was getting hurt apart of the show?”

She shook her head, “No, it was not.”

“So how are we going to tell the council?”

Idris looked up to him with a serious look on her face, “We will not be telling the council.”

He furrowed his brow glaring at her, “You can't exactly hide a pregnancy ambassador.”

“Which is why in 2 months I will be announcing that I have to return to Zero One to which I will have a hovercraft take me and I will have the child there.”

He shook his head, “No not going to happen.”

“You asked me to never to tell anyone.”

“I didn't think you were going to be pregnant!” He sighed calming himself once more, “they will question why you have a child when you return. We must take responsibility to these consequences. I-I also have to tell Clara.”

“We should do it now.”

“Are you feeling well to do it though?”

She sighed and shrugged, “Morning sickness has been a random anomaly that I can not predict so I can not say.”

He nodded holding out his hand to her, “though I can't say I might live after we tell Clara.”

 


	28. Chapter 28

“You what?!” Claras yell was able to be heard in the living area from the bedroom her and the Doctor had chosen to talk in.

The Doctor frowned looking at a very angry Clara, his hands together pleading to her, “Clara, clara. Oh god, I wouldn't had done it if I known.”

Clara glared at him her hands now on her hips, “Yet you would if she couldn't have gotten pregnant?”

 _Oh shit_ , he thought knowing he was now fighting with the full angry female logic that no man has managed to win, “No, fuck, that's not what I meant.”

“So what do you mean? That you needed someone to fuck while I was recuperating after having your children?”

“I was drunk Clara. We both had drank, a lot.”

Clara moved to the door and opened it yelling out into the living area, “Idris get in here!”

“Clara I am telling the truth.”

She shot a glare to Idris, who had fully walked in and closed the door behind her, “What happened on the ship?”

Idris was surprised about the question but answered her, “After my update we proceeded to get intoxicated as the Doctor did not want me to drink alone. I believe the Doctor, in his then growing intoxicated state, was jealous that I was out drinking him till we proceeded to kiss and then have intercourse.” She paused before adding, “Multiple times.”

A loud smack preceded the Doctor stumbling back onto the bed rubbing the very red cheek,“OW!”

Clara yelled at him once more, “Multiple times?!”

Idris backed up a few steps looking down towards the ground this was not what she was expecting from Clara, “Clara it is my fault as well. I was still in control of my actions for most of it but I did not stop myself or him.”

“I can not fucking believe this.” Her hand ran over her face, “we let you into this house to let you learn about humanity not fucking my husband just because now you could.”

“You have not gotten married.”

Clara walked walked furiously up to Idris getting into her face, “We have children he's pretty fucking close to being my husband that I don't care if we're married or not. He is mine.”

Idris put her back up to the wall now looking frightened and now trying to move from Clara, “E-excuse me.” She stumbled off into the nearby bathroom with the sound of heaving coming from it.

Clara glared back the Doctor, “Well at least she's getting the full pregnancy ride.”

The Doctor had a look of concern as he looked towards the bathroom and then sighed looking at Clara, “Clara I do love you very much please, oh please, believe me when I say this.”

“John forgiveness can't be easily given right now.”

He nodded, his hand going back to rubbing his cheek, “I know, I'm stupid I shouldn't have.”

“No you shouldn't.”

 

 

\------

 

The council had all gathered with Idris standing before them, visibly shaken after the incident an hour before. The chairwoman spoke with a soft smile, “I do not see why you needed to tell us? You're pregnant it is a joyous time.”

Idris cocked her head slightly in confusion, “But I am a machine, wouldn't citizens be concerned?”

“Yes you are a machine, a machine who has been accepted into this city as one of our own. You did mention you were as close to a human as a machine would get, the council had a discussion of if that meant that this would happen and agreed that if it did we would accept it like any citizen would.” She smiled looking to Idris, “though it is somewhat amusing that both ambassadors children are fathered by the Doctor.”

Idris looked down towards the floor, “Clara was not happy.”

The council woman nodded, “we're not here to spread around and have as many children as we can Idris. We want to live our lives the way it should be; peaceful and on our own terms.”

Idris nodded, “I understand that more than anything now, even though I do love the Doctor just as much as Clara.”

A man seated a few seats down on the right hand side spoke up, “Excuse me madam chairwoman, may I ask the ambassador a question?”

“Of course Hartnell I am sure she is willing to answer.”

The man stood up, which surprised Idris as he could be heard very clear in the empty chamber, “My curiosity is to how much this child will be machine due to how you've been made, I could only see that the child would be completely human.”

Idris nodded, “you would be correct councilman. Apart from the nanotechnology I will be sharing, the child will be biologically human.”

“Have you been experiencing any symptoms?”

“I will not explain every detail but yes I have. Morning sickness is a most definite, though it should be called hormonal sickness as I have not been experiencing times of illness during the mornings alone.”

The man chuckled for a moment before asking another question, “Apart from being ill how have you been feeling?”

“Happy and afraid.”

“Why have you been afraid?”

“Up until I did not want anything to happen to my child. I was scared to tell the Doctor or the council of my pregnancy. Now I am just afraid of being the best mother.”

The man and a few of the other council members smiled to her answer, “You're on the right track, being worried about being a good mother is the best thing any mother can do.”

Idris started to smile, “Thank you.”

 

\------

 

Idris opened the door of her living quarters seeing the Doctor standing on the walkway with a bag slung over his shoulder, “Doctor what are you doing here?”

The Doctor sighed fighting back tears, “C-clara kicked me out. We happened to have fought again when you went to talk to the council.”

“I do not think it is smart to stay with me especially if you want to amend things with Clara.”

“You're carrying my child, I have a duty of care. Even if it takes me longer to amend things with Clara.”

Idris nodded and opened the door wider letting him inside, “I do not have any other beds.”

He threw the bag onto the sofa after walking over to it, “The sofa is fine.”

She smiled, “would you like to hear it?”

“Hear what?”

She gently took his hand pulling him to her room before letting go to get the device sitting on the nightstand and placing it against her stomach which started to produce an audible quick thudding sound which the Doctor quickly recognized as the fast heart beat of a baby. “I-I fall asleep listening to it.”

“You do?”

“It's silly.”

“No it's not silly.” He walked over putting his hands onto hers and kissing her forehead, “listen to it as much as you want.”

Idris started to laugh with tears streaming down her face, “thank you.”

The Doctor smiled moving a hand up to thumb away the tears, “hey, it's alright.”

Idris nodded, sniffling, “I'm sorry I did this.”

“No don't blame yourself, never blame yourself. What's done is done.” He sighed as the familiar words had been spouted out and then smiled, “work on taking care of yourself and the baby.”

 


	29. Chapter 29

**Notes for the Chapter:**

> A week later.

The Doctor opened the door revealing a small group of red robed women, the sisterhood they were called a bunch of women believing in crazy prophecies and practicing strange rituals. “We wish to see the machine.”

He frowned, “Well first the machine is a she and her name is Idris. So if you want to see her you will address her as such otherwise you can go toddle off to those steam vents of yours.”

“We would like to see Idris, please Doctor.”

He raised an eyebrow surprised of the usage of 'please' but smirked as it was apparent they were wanting to see Idris badly, “Oh much better but I do need to make sure she wants to even see you.”

Idris gently placed her hand on his shoulder slightly startling him, “I want to see them.”

“Are you sure?”

Idris nodded, “I know that most of the city believes this group is of a strange nature but I want to meet them. In fact I asked them to come.”

The sister nodded and smiled as the Doctor opened the door wider albeit hesitantly, “Thank you.”

 

 

The Doctor sat and watched Idris and the sisterhood talk, interestingly enough it did not involve talking about prophecies but about Idris and how she was handling the pregnancy, which intrigued the Doctor as well. He looked over to the eldest sister who had sat down and watched, just as he had, never speaking till now. “How does it feel to father a child mothered by a machine?”

He glared at her, “Idris is far from a machine.”

“All she is is ones and zeroes in a metal casing.”

“Please don't.”

She raised an eyebrow, “Don't what? Tell you the truth of the nature of the hybrid?”

He sat forward towards her, brows furrowed, “Tell me again about that stupid little prophecy of yours because its kind of really vague because you know I have other children. Why aren't you going spastic over them instead?”

“They are twins, human twins.”

He scoffed leaning back, “Oh yes the miracle of zygote splitting, can't be as dangerous as a machine that has a fully functioning reproductive system. It's nothing new they've been doing this for hundreds of years with the fields.”

Her eyes narrowed along with the furrowing of her brow, “You do not understand the seriousness of this.”

“And you do not know how much I have suffered from all the other lies I had blindly followed.” He stood up quickly with his hand pointing to the door, “You have out stayed your welcome please leave.”

Idris looked up to him in surprise, “Doctor?”

The elder stood up nodding, “We will speak again Idris.” The others stood up as well and let themselves out in an orderly fashion.

Idris closed the door and looked back to the Doctor who was still standing next to the table frustrated over what had happened, “Explain.”

“Ohila, the elder woman that was sitting beside me, was trying to get underneath my skin as usual.”

She nodded, “I did partially hear the conversation, she is correct though I am just ones and zeros in a body.”

“I don't think that.” He sighed, “but it isn't about that but what you're carrying.”

Idris frowned, “so they weren't interested in me were they?”

He shook his head, “No.” He sat down looking to her, “they claim themselves as the freeborn version of the oracle, using some of the volcanic steam vents to pretty much get visions, to which you and I know are pretty much hallucinations. Some creepily accurate hallucinations at times.”

“So what does it say?”

“That it will stand in the ruins and destroy a billion billion hearts to heal its own.” He started to chuckle about it, “as I said to her it's vague as hell now as it was when they read it off me.”

Idris cocked her head in confusion and sat down, “Read it off you?”

“It was when they were decent members of society before they tried to overthrow the council. I knew it was just silliness nothing could come about a little palm reading,” he sighed, “worst four years of my life.”

“You know I would never allow anything to happen.”

“Honestly I would not think anything of it. It's vague, like what's the cause? Which ruins? There are plenty of ruins up above us.”

Idris nodded, “agreed.”

 

 

\------

 

 

“Idris!” David ran up to Idris who was standing out front of the door way having just knocked onto it.

“Be careful not too tight.” She smiled as he grabbed her into a hug, “I wanted to come by and talk to Clara.”

“I really have nothing to say,” Clara sternly spoke as she reached the doorway to her home, “David will be over on Wednesday.”

“It's my fault Clara do not blame the Doctor.”

“David can you go inside and tell Andrea to wait a few more minutes,” Clara smirked at Idris waiting for the door to close after David went inside, “Funny he said the same thing about himself so that means you're both to blame especially when he told me everything especially the part how you two woke up the next morning and did it again. Becoming a good human with the lying.”

“I omitted explaining that event but I did say 'multiple times' which was not a lie.”

“And the kiss?”

“We were having a discussion about what I had said about my being practically human. He questioned my heartbeat and I responded with the truth that I had feelings for him.” She looked at Clara who had crossed her arms showing her growing anger towards Idris, “Clara I will not deny the feelings I have had for him only to apologize for what has happened. I believe he should be with you as he has been sleeping on the sofa for the past week and mentioned he has missed his family.”

Clara shook her head, “Why didn't he come over here and say that himself?”

The Doctor spoke up from behind, he had managed to slip up behind listening to the whole conversation, “Because I was afraid you would slap me again plus it was Idris' idea, I would have just stuck to the sofa till something happened.”

“Of course.” Clara sighed, “but you're going to be sleeping on my sofa and changing babies till I fully forgive you.”

The Doctor nodded slowly with a soft smile, “thank you.”

“I know this is still a bad time to make this request,” Idris nervously spoke now, “may I borrow the Doctor in 5 weeks? You may come along as well.”

Clara frowned and then sighed, “it's the ultra sound, right?”

“Correct, in fact I would enjoy your presence along with David.”

“Ask me again as right now it is a bad time.”

Idris nodded, “I understand.”

“Come along Johnathan, I'm pretty sure Rose will need a nappy change.”

The Doctor nodded fearing the horror of what a four month old could do in a diaper, “Yes of course.”

 


	30. Chapter 30

Idris sat in the small little waiting room in the medical wing, she was waiting more on the Doctor and Clara than the staff who had been running behind. A few other people had made glances towards her, some with intrigue and some still scared of what she was. She gently ran her hand over the spot the baby was pushing against, she had felt the then flutter a few weeks ago but to feel it inside and against her hand was an interesting feeling.

“How long?” A very pregnant woman near by quietly spoke up breaking the the awkward quietness of the room.

Idris looked over trying to not act surprised that someone would strike up a conversation with her, she didn't blame them as she mainly stayed to her home and to typical places of the market, “How long have I been or how long do I have left?”

The brunette haired woman smiled, “You pick.”

“I'm 21 weeks.”

“Mines almost over due like the last two have been, they're all stubborn like their father.”

Idris smiled for a moment and then frowned looking back down to her stomach, father – it's father – the Doctor.

“Oh I'm sorry I hope I didn't upset you?”

Idris shook her head, “No, no I am just – I do not know the emotion.”

The woman smiled once more, “Sadly pregnancy does that gives you all the emotions at the same time, it's alright. What do you want it to be?”

“I never thought about gender I would be happy that it will be healthy, happy and someone that I was proud to have raised.”

“I'd never thought I would hear that from a machine.” She chuckled nervously, “sorry.”

Idris smiled softly, “I understand. I am grateful of your curiosity.”

“But what would you like it to be? If you thought about it.”

Idris smiled more almost into a grin, “A boy, I want it to be like his father.” She looked back up, “what are you going to have?”

“A girl, finally.” She giggled a little, “we originally wanted just two but when they both ended up being boys we decided it would be okay to try for a girl.”

“Were you scared the first time?”

The woman smiled, “Depends on which part you mean. I was happy to having a child with someone I loved but when the time came closer, oh yes I was scared. Scared of being a good mother, hell even with the labor I was scared but once that baby was in my arms,” she paused then started to giggle, “I was glad it was done and wanted to take a nap.”

Idris started to softly laugh with her, “thank you.”

“No thank you. It was nice to actually talk to you instead of be talked to by you.”

Idris looked surprised, “should I talk to more people?”

The woman nodded, “yes though with someone with you I would hate to have another incident happen with you.”

“Of course.”

 

\------

 

 

Idris stared at the door to Clara and the Doctors living quarters, they had not shown up even with the extra hour of waiting before she had even been called in. She sighed remembering how Clara acted when she had come around to remind them of the day a week back she had still seemed upset of the situation but still decided to knock on the door.

The door opened revealing Clara in a slight surprise to who was at the door then frowned, “Oh it was today wasn't it?”

Idris nodded, looking down and handing over the printouts, “here, you can give them to him or not.”

Clara reached out grabbing not for the pictures for Idris' hand, “no come inside.”

“Are you sure?”

“Yes because the last few weeks the twins have been teething and cranky and really had been just living through one day at a time. We all honestly forgot.”

“You're not mad at me?”

Clara shook her head, “Not as much as I was but it's been done, John has changed enough diapers to impress me and you,” Clara sighed, “you're pregnant I think that's a punishment in itself especially after the baby gets here.” She waved Idris inside, “come in I know you want to share those.”

“Thank you, in fact I want you to see them first. I had the nurse put the gender on one of these and I don't know yet I wanted to share it with you.” She held the pictures out again to Clara who took them looking at the top one and smiled.

“Did you want to know the gender?”

“If you want to tell me now that is fine.”

“Tell about what?” He looked down into Claras hands looking at the ultrasound pictures, “oh I missed it.”

“I was upset thinking Clara was still upset with me and had asked you to stay but after what Clara had told me I understand.” She nodded to the pictures, “I haven't seen what the baby is going to be I wanted you, especially Clara to know first.”

The Doctor took the pictures of her hands and looked at them smiling, “I can't wait to meet him.”

Idris perked up, “It's a boy?”

He nodded and held the picture up, “see?”

Idris smiled, “is it odd to say I had a feeling it would be?”

The Doctor laughed and then realized they were still standing at the door, “come in I bet you need to sit down or lay down.”

Idris nodded, “I am tired yes.”

Clara smirked, “eaten yet?”

“No but I can do that when I get home.”

Clara smirked, “you lived here for a while I think this can count as home to you as well. Eat, take a nap if you need to, and see the twins even.”

“Thank you.” Idris smiled as she stepped in, “this means a lot to me.”

 


	31. Chapter 31

“I'm thinking of asking Jack to help check in on Idris. It's the last month and I don't want her to be alone when it's time.” The Doctor looked over to Clara as they laid in bed enjoying the longer nights of rest from the twins.

She smirked, “I was actually thinking of asking her to stay here. It would be easier for her.”

He raised an eyebrow in surprise, “Are you sure?”

“Yes, I was honestly happy when I went into labor with you with me.”

“You were?”

She giggled, “Yeah, I had been somewhat scared that I would be alone.”

He rolled over putting his arms gently around her, “you know I would have felt awful if that happened.”

She nodded, “I know, I've know after every time somethings happened to her and to me.”

He smiled kissing her on the cheek, “Want to have more?”

Clara rolled her eyes, “I don't think I'm ready for 3 hours of sleep again and you have to help her with your son.”

He chuckled, “I know but babies they're so wonderful.”

“Something must be wrong with you. Even after making you change twins for two months you say babies are wonderful?”

The Doctor rolled back onto his back and sighed, “Okay you have me there."

She grinned rolling over climbing on top of him, “ask me later though, especially after we have had a full nights sleep for at least a year,” leaning down to gently kiss him on the lips.

 

\------

 

 

“That is a generous offer but I will be fine Doctor. You already have a full residence with the twins and David.” Idris smiled as she sat on the sofa casually playing at the corner of a pillow her arm was rested on.

The Doctor looked at her with some interest as he sat next to her, “you sure? I don't want you to be alone if you go into labor.”

She nodded, “I have already made plans and preparations for when the time comes. I would still enjoy if you did stop by more often.”

“I doubt Clara would have any problem with that. If I can't would you be alright with Jack coming over as well? I will have to ask him.”

“Of course I haven't seen him as much as I would like.”

“He's been the operator for the Paternoster for the last few months actually, just got back.”

Idris smiled, “I'm still amused there are more ships out now than before the treaty.”

“Well saying we got the go ahead with being a little more open to the blue pills we've had to have a lot more people out there answering questions and pulling people out.”

She nodded and casually ran her hand over her stomach almost like she had not listened to what the Doctor had said.

“Everything alright?

“Yes of course apologies he was moving.”

The Doctor chuckled softly and then reminded himself of a much important question, “Oh what were you thinking of for a name?”  
  
She grinned looking over to him, “I was hoping that I could name him after you and I know you're possibly wondering why I would name a child 'Doctor' I was not; I wanted to name him John.”

“I'm, wow, really?”

She nodded, “Yes.”

“Reason?”

“He is your son and I would enjoy it if he grew up being the same as his father, a kind man that cares for everyone.”

His hand covered his mouth in surprise, he knew he had made an impression to Idris but to hear it was something that he knew he had to live up to, “Wow.”

“Is it alright?”

He nodded quickly and excitedly, “Y-yeah, yeah very much so.”

 

\-------

 

The Doctor opened the door after knocking a few times, he knew Idris wouldn't have left home without leaving a note, poking his head into the room, “Idris?”

Her voice came from the other room, “I'm in the bathroom.”

He walked over and peered inside the semi dark room seeing her laying in the metal bathtub with a few candles lit around, he had questioned why she had needed them a week ago but now he knew and figured she was quietly relaxing, “Oh, I'm sorry to have barged in.”

“No it is not a problem,” Idris paused to groan in pain gripping the side for a minute before continuing her sentence, “this is an alright time to do such a thing.”

The Doctor stepped inside trying to get a better look under the dim light of the candles, he knew that sound all too well from Clara, “A-are you in labor?”

She spoke softly, tiredness was creeping into her voice, “Yes, have been for the past 5 hours now.”

“Why didn't you go to medical?”

“I wanted it to be here, more relaxing. The doctor was perfectly okay with me doing this.”

The Doctor frowned moving to kneel next to her, “Well I'm not what happens if something goes wrong?”

She smirked, “I have you.”

The Doctor nervously chuckled, “remember what happened last time? I had a bruise for a month.”

She finally looked up still smirking to him, “I meant for you to run to medical, if it was needed.”

The Doctor sighed, he didn't know how this would go over especially with someone who never had a child before and someone who fainted at the sight of blood, “Did you need anything?”

She groaned once more as another contraction made its way through,“Just be here.”

“Okay.” He gently took her hand that was going to go back into the warm water of the tub and held it.

She pulled her hand away. “Holding your hand would not be a wise idea, I would break it. I think I already put dents into the metal here.”

“Right... right.” He sighed trying to figure out something to help, even though she had only asked him to be there, he blurted out,“why water?”

“It actually is relaxing but now it's getting worse I do not know if I can endure more.”

“You got through five hours of this so far and I'm here now.”

“Yes but,” another pause to breathe with another groan at the end, “it did not hurt as much as it does now.”

“That just means he's coming. Clara said the same thing right before the nurses said it was time to push.” He watched her move, the lights not reaching into the water so he couldn't see how she was seated now, grabbing hold of the tub with both hands, “did you need a hand?”

“I needed to move, I am,” she cried out in pain the last of the sentence this time around, “fine.”

“Doesn't sound like it.”

“That's because I think you're right and he's coming,” she cried out once again, “hurts.”

He set his hand on her back gently rubbing over it, “Just breathe and push through it. He'll be here soon.”

The Doctor spoke to her helping her along while trying to remember what was said with Clara, soon felt almost like forever till a gasp came out and she sat back down picking the child up out of the water cradling it against her chest, “L-look, look at you,” she gasped as the tears welled in her eyes as the babe started to wail, “look what I did my thief, look.”

The Doctor was in shock as he heard the first cries of his son, he had been knocked out on the floor for both of his daughters, “yes, yes look at what we did Idris.”

 

 

 

The Doctor sat with the swaddled baby in the living area cradling him, he had felt something strange yet familiar on the base of the childs neck, feeling for a few more moments before actually looking he realized it was a connection port. “Idris, he has a connection port on the back of his neck.”

She yelled out from the bathroom, “The nanites made it, you missed seeing it on the pictures.”

“Did you know this would happen?”

“Yes.”

The Doctor smirked holding him out in front of him softly speaking, “would have been nice to know.” He then smiled as the small bundle wiggled before opening his eyes trying to look at his surroundings in curiosity revealing that he did not have the standard blue eyes all newborns had but silver. The Doctor raised an eyebrow and spoke up, “what about silver eyes?”

Idris slowly came out with a robe on after cleaning up, sitting down she leaned against him as they both looked at their son, “That is interesting.”

“Think it will change?”

“I do not know,” her hand gently ran against the curve of the babys head, “but we will make sure he is treated like everyone else.”

The Doctor nodded and then kissed the top of Idris' head, “get some sleep you did a lot today.”

 


	32. Chapter 32

Johns silver eyes glared at the source who stood above him looking down to the near identical son of the Doctor, he had known growing up he would be here at some point and 18 years later as his RSI stood in front of it in the matrix.

The source finally spoke its voice booming it's one word, “Flawed.”

He scoffed and smirked, “Dumbass.”

“Explain.”

John pointed to himself, “I'm not flawed I am far from flawed. I was made by two great people on this world, one which you sent to make you a special little baby for you to control.” He grinned, “Sorry about your luck but you should have known my parents a little better.” John saw the code move around meticulously as it gave away that the source was unsure of what to do and was trying hard to use resources to figure out it's next step,“Don't know what to say do you? You know you messed up and now you're trying to figure out how to fix it. I wouldn't suggest trying to send another 'ambassador' because well you have two now and the council will get very concerned on what your big plan is.”

“The human infestation is out of control it must be contained.”

He raised his arms up as he finally got the answer that his parents warned him about, “There it is. We've come full circle.”

“You do not understand.”

“I don't understand?” He shouted, “OH BOY. I was told the stories, on both sides in fact, I grew up being bullied for being what I was and especially who my parents are. Fuck yes I understand but to wipe out humans just because you still hate them for all they did. No _THAT_ is unacceptable.”

If it had facial features the source would have raised an eyebrow to the hybrid beneath him, “Do you have another plan?”

“To deal with it. So far you've done a good job for almost 20 years I mean we can go back playing the cat and mouse game of us dodging agents while we pull out people who want out if that's what you want?” He shrugged, “I mean honestly I think right now it's easier to find the One the way it is now and we could all work together to clear up that sky if it's all possible.”

“Why do you care so much?”

“Because like my father I'm a Doctor now. So make up your mind you're wasting my time.”

It shook its head, “Unacceptable, as you said it will come full circle.”

“As you wish.” He pulled out a new design of a mobile phone and hit the speed dial, “Pop it.”

The source looked around as all the monitors changed to a video of the young man standing in ruins, “How did you do this?”

“Remember I'm part you, one hell of a virus maker and you just let me walk on in here with it. Enjoy.” He grinned as he disappeared in a flash of light.

The source stood, it's glowing code furiously streaming attempting to destroy the virus that was streaming the video to everyone and every machine in the matrix.

 

_Citizens of Earth or what you think is Earth, behind me stands the ruins of what really is and what you stand, sit or lay down upon really isn't. Your lives are a lie as you mingle around the virtual reality known as the Matrix. I am the Doctor and I am here to set you finally free._

 

 

**Notes for the Chapter:**

> I apologize for the cheesey ending as I was seriously hung up on how to continue it.


End file.
